from google.colab import drive
'/content/drive') drive.mount(
Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).
from google.colab import drive
'/content/drive') drive.mount(
Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).
!pwd
/content
import os
# checking if the directory demo_folder
# exist or not.
= "/content/drive/MyDrive/design_build"
design_build_dir if not os.path.exists(design_build_dir):
# if the demo_folder directory is not present
# then create it.
os.mkdir(design_build_dir) os.chdir(design_build_dir)
!pwd
/content/drive/MyDrive/design_build
def udocker_init():
import os
if not os.path.exists("/home/user"):
!pip install udocker > /dev/null
!udocker --allow-root install > /dev/null
!useradd -m user > /dev/null
print(f'Docker-in-Colab 1.1.0\n')
print(f'Usage: udocker("--help")')
print(f'Examples: https://github.com/indigo-dc/udocker?tab=readme-ov-file#examples')
def execute(command: str):
= "\033[1;32muser@pc\033[0m"
user_prompt print(f"{user_prompt}$ udocker {command}")
!su - user -c "udocker $command"
return execute
= udocker_init() udocker
Docker-in-Colab 1.1.0
Usage: udocker("--help")
Examples: https://github.com/indigo-dc/udocker?tab=readme-ov-file#examples
!udocker --allow-root pull broadinstitute/gatk:4.5.0.0
Info: downloading layer sha256:a0350cd371d6d1507fc4cf617e175eb5bd4c3b204c333c94d185bf1ea0795e28
Info: downloading layer sha256:0ed77206bc58a5c4253dc48f63c49ae2f6a3dfef68374e35b8906e397b8b3a34
Info: downloading layer sha256:4da44515c0282c753dea8e5d620f840683b9be744fc3558aa200a3b6801d6d02
Info: downloading layer sha256:a3d1f390828eebbdf0dd57dde549378ccefa065824953f433e83a7c90782f18d
Info: downloading layer sha256:e28bcb90193018e21503133c0c383ae7124a6407a607045140b41cf81f2eb850
Info: downloading layer sha256:0258c7d63f9241bccdb6655a641406158b0a0d6cedc40219f8f8eb98d84590ba
Info: downloading layer sha256:b3625edcebc02c6a07a068a9bb09e929f281041bf1929c3fc914e22a01c7db76
Info: downloading layer sha256:8744436b9dbf91ddefe776c5aa6d061fa93655ff265edc3c6cfcd2ca5398e5e0
Info: downloading layer sha256:f34824c486eb930b1bf0bdd34c45fbb7d237e6c22fdaf716a65c9e9a2fc6f194
Info: downloading layer sha256:4f084384c353a3bf1e2d8a7c6855261feced9060e1ccfcb572243777d87b5741
Info: downloading layer sha256:891945c414afb02f8aa7f1ca2688134147fdd3f8108372851fbb996c3c96d8b2
Info: downloading layer sha256:cffcd2ae2fcdfcfb2ee1886960f2a4fffdc20d4f7a53ea5cb8b107fce7f2acdd
Info: downloading layer sha256:cf7105ec9c451c3c31b518f90a63fcd21e409dcf99a8c23c2e6b45fb0e3404ef
Info: downloading layer sha256:134b348e3b5e7720f8e80c492939d15d4b15338fb03cd3417a651c0d79b7f6aa
Info: downloading layer sha256:5bb37dfbacf38a543a3b8322ede27dc48c7abd9346a53633913c95356d1ca32e
Info: downloading layer sha256:90226c0b8ca9b1c5bdfb48f0625f151e2acbffcf793aad9319f81fa795749236
Info: downloading layer sha256:91e6f2d6d5602796597c6b4f77786421b207d0746b8265ead7357f543facbc02
Info: downloading layer sha256:762ff3861584e4482f79ebaeef7c0a5b5fd2f6ce91d9190b54353b614a5e2b26
Info: downloading layer sha256:043eca7b7dd5fb53ae84f5e3e94d3bdee177fbfe702bfef8502ccf5062794939
Info: downloading layer sha256:1a799190d815f77920c9963278e0e8b1a3c2f66bf5850bc46ce6fb9da3273258
Info: downloading layer sha256:5e8117c0bd28aecad06f7e76d4d3b64734d59c1a0a44541d18060cd8fba30c50
!udocker --allow-root pull staphb/minimap2:2.28
Info: downloading layer sha256:858eac332b979bf2408f3c3c67dd281593cb8219212009d75944e0fbfc8a93a1
Info: downloading layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1
Info: downloading layer sha256:c4c71a0bb4e0776f27a061207311a5b51348e03aa9fa0b71783d1c647431536a
Info: downloading layer sha256:b3d5e5561d0719e43f9195e30076f07b92c6552dc888d4f9a62b9d47100c38f1
Info: downloading layer sha256:bccd10f490ab0f3fba61b193d1b80af91b17ca9bdca9768a16ed05ce16552fcb
!udocker --allow-root images -l
REPOSITORY
broadinstitute/gatk:4.1.3.0 .
/root/.udocker/repos/broadinstitute/gatk/4.1.3.0
/sha256:b48fdadebab0cc3a4ed00c1f522658ebb68047690d1426a98bbdfec9dff1755b (384 MB)
/sha256:5ad56d5fc14905886c560200ab69f905b5c5287eaf12f8f761a7ab54f7a61c1b (0 MB)
/sha256:16fb14f5f7c998f3cdd435d57a870e25866d6856f3e94ed8f37ebc452c37e5b8 (988 MB)
/sha256:395460e233f5bdcd910d618a3b615e0d881e09ad27d58f3065eef53ecae6a808 (0 MB)
/sha256:170e558760e8b2e484a022b7d7272cf284fc4e1936ba7a0a671fc586440ad272 (0 MB)
/sha256:ae79f251470513c2a0ec750117a81f2d58a50727901ca416efecf297b8a03913 (45 MB)
/sha256:0ef3d00baa098a5253ed18b54451748d16e9d0e26f32d7f4eac882640afe89ac (0 MB)
/sha256:6f01dc62e444044e3ce494269837ef0aedb80fef69c679416137f17812d2eb9c (0 MB)
broadinstitute/gatk:4.5.0.0 .
/root/.udocker/repos/broadinstitute/gatk/4.5.0.0
/sha256:cf7105ec9c451c3c31b518f90a63fcd21e409dcf99a8c23c2e6b45fb0e3404ef (701 MB)
/sha256:1a799190d815f77920c9963278e0e8b1a3c2f66bf5850bc46ce6fb9da3273258 (363 MB)
/sha256:762ff3861584e4482f79ebaeef7c0a5b5fd2f6ce91d9190b54353b614a5e2b26 (49 MB)
/sha256:4da44515c0282c753dea8e5d620f840683b9be744fc3558aa200a3b6801d6d02 (0 MB)
/sha256:8744436b9dbf91ddefe776c5aa6d061fa93655ff265edc3c6cfcd2ca5398e5e0 (0 MB)
/sha256:891945c414afb02f8aa7f1ca2688134147fdd3f8108372851fbb996c3c96d8b2 (0 MB)
/sha256:5e8117c0bd28aecad06f7e76d4d3b64734d59c1a0a44541d18060cd8fba30c50 (28 MB)
/sha256:a3d1f390828eebbdf0dd57dde549378ccefa065824953f433e83a7c90782f18d (0 MB)
/sha256:134b348e3b5e7720f8e80c492939d15d4b15338fb03cd3417a651c0d79b7f6aa (0 MB)
/sha256:4f084384c353a3bf1e2d8a7c6855261feced9060e1ccfcb572243777d87b5741 (0 MB)
/sha256:5bb37dfbacf38a543a3b8322ede27dc48c7abd9346a53633913c95356d1ca32e (0 MB)
/sha256:043eca7b7dd5fb53ae84f5e3e94d3bdee177fbfe702bfef8502ccf5062794939 (0 MB)
/sha256:f34824c486eb930b1bf0bdd34c45fbb7d237e6c22fdaf716a65c9e9a2fc6f194 (0 MB)
/sha256:b3625edcebc02c6a07a068a9bb09e929f281041bf1929c3fc914e22a01c7db76 (0 MB)
/sha256:0258c7d63f9241bccdb6655a641406158b0a0d6cedc40219f8f8eb98d84590ba (0 MB)
/sha256:cffcd2ae2fcdfcfb2ee1886960f2a4fffdc20d4f7a53ea5cb8b107fce7f2acdd (0 MB)
/sha256:a0350cd371d6d1507fc4cf617e175eb5bd4c3b204c333c94d185bf1ea0795e28 (0 MB)
/sha256:0ed77206bc58a5c4253dc48f63c49ae2f6a3dfef68374e35b8906e397b8b3a34 (1095 MB)
/sha256:e28bcb90193018e21503133c0c383ae7124a6407a607045140b41cf81f2eb850 (0 MB)
/sha256:90226c0b8ca9b1c5bdfb48f0625f151e2acbffcf793aad9319f81fa795749236 (0 MB)
/sha256:91e6f2d6d5602796597c6b4f77786421b207d0746b8265ead7357f543facbc02 (123 MB)
!udocker --allow-root create --name=gatk broadinstitute/gatk:4.5.0.0
43258f40-d39f-316f-8a89-594ce69950cc
!udocker --allow-root create --name=minimap2 staphb/minimap2:2.28
b3f70d3a-fd01-3b04-a386-87cfbbf7c997
!udocker --allow-root ps
CONTAINER ID P M NAMES IMAGE
43258f40-d39f-316f-8a89-594ce69950cc . W ['gatk'] broadinstitute/gatk:4.5.0.0
b3f70d3a-fd01-3b04-a386-87cfbbf7c997 . W ['minimap2'] staphb/minimap2:2.28
0e74f2dd-6e30-3ea9-b8c0-bf38ddc81fe4 . W broadinstitute/gatk:4.1.3.0
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk ls -al /design_build
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: ls
total 82809
-rw------- 1 root root 18903978 Jun 4 03:50 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
-rw------- 1 root root 19758840 Jun 4 03:50 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
drwx------ 2 root root 4096 Jun 4 03:53 bam
drwx------ 2 root root 4096 Jun 4 03:53 info
-rw------- 1 root root 466 Jun 4 10:33 mapping_stats.log
-rw------- 1 root root 16343 Jun 4 16:34 my.vcf
-rw------- 1 root root 277 Jun 4 16:34 my.vcf.idx
-rw------- 1 root root 15019 Jun 4 03:50 pACBB-PL-from_EcoRI_hs.gb
-rw------- 1 root root 108 Jun 4 16:00 pACBB_PL.dict
-rw------- 1 root root 7363 Jun 4 07:20 pACBB_PL.fasta
-rw------- 1 root root 23 Jun 4 13:58 pACBB_PL.fasta.fai
-rw------- 1 root root 9280 Jun 3 04:26 pUC19-J23100.gb
-rw------- 1 root root 8592 Jun 3 04:26 pUC19-L2U3H03.gb
-rw------- 1 root root 9040 Jun 3 04:27 pUC19-RB0030.gb
-rw------- 1 root root 11934 Jun 3 04:27 pUC19-egfp.gb
-rw------- 1 root root 46033492 Jun 4 16:18 reads_with_RG.bam
-rw------- 1 root root 96 Jun 4 16:19 reads_with_RG.bam.bai
-rw------- 1 root root 16 Jun 4 13:58 regions.bed
drwx------ 2 root root 4096 Jun 4 03:53 sam
drwx------ 2 root root 4096 Jun 4 10:23 sort
!wget https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/parts/pACBB-PL-from_EcoRI_hs.gb
!wget https://github.com/greendaygh/kaist_design_build_2024/raw/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
!wget https://github.com/greendaygh/kaist_design_build_2024/raw/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
--2024-06-05 01:53:18-- https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/parts/pACBB-PL-from_EcoRI_hs.gb
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15019 (15K) [text/plain]
Saving to: ‘pACBB-PL-from_EcoRI_hs.gb’
pACBB-PL- 0%[ ] 0 --.-KB/s pACBB-PL-from_EcoRI 100%[===================>] 14.67K --.-KB/s in 0.002s
2024-06-05 01:53:18 (7.83 MB/s) - ‘pACBB-PL-from_EcoRI_hs.gb’ saved [15019/15019]
--2024-06-05 01:53:19-- https://github.com/greendaygh/kaist_design_build_2024/raw/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
Resolving github.com (github.com)... 140.82.114.4
Connecting to github.com (github.com)|140.82.114.4|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz [following]
--2024-06-05 01:53:19-- https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 18903978 (18M) [application/octet-stream]
Saving to: ‘FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz’
FAT01036_pass_barco 100%[===================>] 18.03M 51.8MB/s in 0.3s
2024-06-05 01:53:19 (51.8 MB/s) - ‘FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz’ saved [18903978/18903978]
--2024-06-05 01:53:19-- https://github.com/greendaygh/kaist_design_build_2024/raw/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz [following]
--2024-06-05 01:53:20-- https://raw.githubusercontent.com/greendaygh/kaist_design_build_2024/main/data/fastq/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19758840 (19M) [application/octet-stream]
Saving to: ‘FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz’
FAT01036_pass_barco 100%[===================>] 18.84M 36.2MB/s in 0.5s
2024-06-05 01:53:20 (36.2 MB/s) - ‘FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz’ saved [19758840/19758840]
!ls -alh
total 37M
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
-rw------- 1 root root 15K Jun 5 01:53 pACBB-PL-from_EcoRI_hs.gb
!pip install pydna
!pip install biopython
Collecting pydna
Downloading pydna-5.2.0-py3-none-any.whl (115 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 115.9/115.9 kB 3.2 MB/s eta 0:00:00
Collecting appdirs>=1.4.4 (from pydna)
Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Collecting biopython>=1.80 (from pydna)
Downloading biopython-1.83-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 13.1 MB/s eta 0:00:00
Requirement already satisfied: networkx>=2.8.8 in /usr/local/lib/python3.10/dist-packages (from pydna) (3.3)
Requirement already satisfied: prettytable>=3.5.0 in /usr/local/lib/python3.10/dist-packages (from pydna) (3.10.0)
Collecting pyfiglet>=0.8.post1 (from pydna)
Downloading pyfiglet-1.0.2-py3-none-any.whl (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 18.8 MB/s eta 0:00:00
Requirement already satisfied: pyperclip>=1.8.2 in /usr/local/lib/python3.10/dist-packages (from pydna) (1.8.2)
Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython>=1.80->pydna) (1.25.2)
Requirement already satisfied: wcwidth in /usr/local/lib/python3.10/dist-packages (from prettytable>=3.5.0->pydna) (0.2.13)
Installing collected packages: appdirs, pyfiglet, biopython, pydna
Successfully installed appdirs-1.4.4 biopython-1.83 pydna-5.2.0 pyfiglet-1.0.2
Requirement already satisfied: biopython in /usr/local/lib/python3.10/dist-packages (1.83)
Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython) (1.25.2)
from pydna.readers import read
= read("pACBB-PL-from_EcoRI_hs.gb")
records display(records.list_features())
/usr/local/lib/python3.10/dist-packages/Bio/GenBank/Scanner.py:1528: BiopythonParserWarning: Attempting to parse malformed locus line:
'LOCUS pACBB-PL-from_Ec 7214 bp DNA circular SYN 02-JUN-2024\n'
Found locus 'pACBB-PL-from_Ec' size '7214' residue_type 'DNA'
Some fields may be wrong.
warnings.warn(
/usr/local/lib/python3.10/dist-packages/Bio/SeqFeature.py:230: BiopythonDeprecationWarning: Please use .location.strand rather than .strand
warnings.warn(
Ft# | Label or Note | Dir | Sta | End | Len | type | orf? |
---|---|---|---|---|---|---|---|
0 | nd | --> | 0 | 7214 | 7214 | source | no |
1 | L:L1U4H07 | --> | 133 | 162 | 29 | misc_feature | no |
2 | L:opd | <-- | 169 | 1144 | 975 | CDS | yes |
3 | L:BBa_0034 | <-- | 1148 | 1169 | 21 | misc_feature | no |
4 | L:BBa J23100 | <-- | 1173 | 1208 | 35 | misc_feature | no |
5 | L:L3S1P56 | --> | 1326 | 1378 | 52 | misc_feature | no |
6 | L:dmpR | <-- | 1385 | 3074 | 1689 | CDS | no |
7 | L:BBa_B0032 | <-- | 3078 | 3100 | 22 | misc_feature | no |
8 | L:BBa_J23103 | <-- | 3104 | 3138 | 34 | promoter | no |
9 | L:Po | --> | 3250 | 3421 | 171 | misc_feature | no |
10 | L:BBA_B0030 | --> | 3425 | 3449 | 24 | misc_feature | no |
11 | L:sfGFP | --> | 3454 | 4168 | 714 | CDS | no |
12 | L:L3S1P56 | --> | 4175 | 4226 | 51 | misc_feature | no |
13 | L:CmR | <-- | 5250 | 5910 | 660 | CDS | yes |
14 | L:cat promoter | <-- | 5910 | 6013 | 103 | promoter | no |
15 | L:p15A ori | <-- | 6538 | 7083 | 545 | rep_origin | no |
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
# SeqRecord(records)
print(records)
= SeqRecord(
record
records.seq,id="pACBB_PL",
="for part assembly"
description
)
"pACBB_PL.fasta", "fasta") SeqIO.write(record,
Dseqrecord
circular: True
size: 7214
ID: .
Name: pACBB-PL-from_Ec
Description: synthetic circular DNA
Number of features: 16
/molecule_type=DNA
/topology=circular
/data_file_division=SYN
/date=02-JUN-2024
/accessions=['.']
/keywords=['']
/source=synthetic DNA construct
/organism=synthetic DNA construct
/taxonomy=[]
/references=[Reference(title='Direct Submission', ...)]
Dseq(o7214)
AATT..GATG
TTAA..CTAC
1
!ls -alh
total 37M
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
-rw------- 1 root root 7.2K Jun 5 01:56 pACBB_PL.fasta
-rw------- 1 root root 15K Jun 5 01:53 pACBB-PL-from_EcoRI_hs.gb
import os
= "/content/drive/MyDrive/design_build/sam"
sam_dir = "/content/drive/MyDrive/design_build/bam"
bam_dir = "/content/drive/MyDrive/design_build/info"
info_dir = "/content/drive/MyDrive/design_build/sort"
sort_dir
if not os.path.exists(sam_dir):
os.mkdir(sam_dir)if not os.path.exists(bam_dir):
os.mkdir(bam_dir)if not os.path.exists(info_dir):
os.mkdir(info_dir)if not os.path.exists(sort_dir):
os.mkdir(sort_dir)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build minimap2 bash -c "minimap2 \
-ay /design_build/pACBB_PL.fasta \
/design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz > \
/design_build/sam/0.sam"
******************************************************************************
* *
* STARTING b3f70d3a-fd01-3b04-a386-87cfbbf7c997 *
* *
******************************************************************************
executing: bash
[M::mm_idx_gen::0.014*0.37] collected minimizers
[M::mm_idx_gen::0.015*0.46] sorted minimizers
[M::main::0.015*0.46] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.015*0.47] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.015*0.47] distinct minimizers: 1270 (98.27% are singletons); average occurrences: 1.034; average spacing: 5.494; total length: 7214
[M::worker_pipeline::13.192*1.42] mapped 4000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
[M::main] Real time: 13.194 sec; CPU: 18.793 sec; Peak RSS: 0.263 GB
from glob import glob
= ["/design_build/"+fn for fn in glob(f"*.fastq.gz")]
fastq_filenames print(fastq_filenames)
['/design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz', '/design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz']
from glob import glob
## -------
= ["/design_build/"+fn for fn in glob(f"*.fastq.gz")]
fastq_filenames = [fn.replace(".fastq.gz", ".sam").replace("/design_build/", "/design_build/sam/") for fn in fastq_filenames]
sam_filenames ## -------
= zip(fastq_filenames, sam_filenames)
zipdata = "/design_build/pACBB_PL.fasta"
reference_filename #print(list(zipdata))
for fnfile, samfile in zipdata:
= f"minimap2 -ay {reference_filename} {fnfile} > {samfile}"
exestr print(exestr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build minimap2 bash -c "{exestr}"
minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz > /design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.sam
******************************************************************************
* *
* STARTING b3f70d3a-fd01-3b04-a386-87cfbbf7c997 *
* *
******************************************************************************
executing: bash
[M::mm_idx_gen::0.012*0.45] collected minimizers
[M::mm_idx_gen::0.013*0.55] sorted minimizers
[M::main::0.013*0.55] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.013*0.56] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.013*0.56] distinct minimizers: 1270 (98.27% are singletons); average occurrences: 1.034; average spacing: 5.494; total length: 7214
[M::worker_pipeline::12.149*1.55] mapped 4000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
[M::main] Real time: 12.150 sec; CPU: 18.809 sec; Peak RSS: 0.263 GB
minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz > /design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.sam
******************************************************************************
* *
* STARTING b3f70d3a-fd01-3b04-a386-87cfbbf7c997 *
* *
******************************************************************************
executing: bash
[M::mm_idx_gen::0.011*0.44] collected minimizers
[M::mm_idx_gen::0.013*0.51] sorted minimizers
[M::main::0.013*0.51] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.013*0.51] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.013*0.52] distinct minimizers: 1270 (98.27% are singletons); average occurrences: 1.034; average spacing: 5.494; total length: 7214
[M::worker_pipeline::11.232*1.77] mapped 4000 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
[M::main] Real time: 11.233 sec; CPU: 19.912 sec; Peak RSS: 0.227 GB
!ls -al sam/
total 116192
-rw------- 1 root root 39055100 Jun 5 02:04 0.sam
-rw------- 1 root root 39055100 Jun 5 02:15 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.sam
-rw------- 1 root root 40868986 Jun 5 02:15 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.sam
sam_filenames
['/design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.sam',
'/design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.sam']
= sam_filenames[0].replace("_0", "_merged")
merged_samfile = " ".join(sam_filenames)
sam_files_str
= f"samtools merge -f {sam_files_str} -o {merged_samfile}"
execstr #print(execstr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{execstr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
! ls -alh sam/
total 186M
-rw------- 1 root root 38M Jun 5 02:04 0.sam
-rw------- 1 root root 38M Jun 5 02:15 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.sam
-rw------- 1 root root 39M Jun 5 02:15 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.sam
-rw------- 1 root root 73M Jun 5 02:24 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged.sam
!head -n 20 sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged.sam
@HD VN:1.6 SO:unsorted GO:query
@SQ SN:pACBB_PL LN:7214
@PG ID:minimap2 PN:minimap2 VN:2.28-r1209 CL:minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
@PG ID:minimap2-4B3706C2 PN:minimap2 VN:2.28-r1209 CL:minimap2 -ay /design_build/pACBB_PL.fasta /design_build/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
@PG ID:samtools PN:samtools PP:minimap2-4B3706C2 VN:1.13 CL:samtools merge -f -o /design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged.sam /design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.sam /design_build/sam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.sam
c8444849-ddea-4bed-b1df-80b1981aac85 0 pACBB_PL 4292 60 112S108M1D54M1I1M1I50M2I43M1D73M2D21M1D32M3I36M1D86M2I5M1I4M2D10M1D13M2I4M2D25M1D5M1D110M1D11M3I19M1D4M1D49M3D31M2I3M2I2M1D5M2D4M1I90M1I74M2I7M2I70M2I19M1D2M1D4M1D12M1D48M1I54M2I1M1D10M2D2M2D4M3D2M1I2M1I8M1I6M2D20M1I12M2D5M1D19M1D5M1D23M2D2M1I6M1D12M2I34M1D7M1I30M3D15M1D11M1D8M3D11M1D7M1D101M1D48M1D50M3D24M2D58M5I74M1D1M1D24M2I18M3D68M1I5M2D3M1D9M2D51M1D49M2D4M1D51M2D59M1D1M1D17M1I17M1D27M4D50M2I8M1D3M2D18M2I3M1D70M1D5M1I35M1D88M1D1M1D17M3D47M1D43M3D38M1I7M1D6M1D7M4D72M3I22M3D2M1D1M3I40M1D20M5S * 0 0 AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCCAGTGAGCCTTGAGACCTTTACACTTTACAAGTAAAGGTCTCTTCGCATAGTGAGACGATTCTCCTTACACATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCGGGCAGCGTTGGGTCCTGGCCACGGGTACGCTGATCGTGCTCCTGCCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGCGATTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTACACAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTTGGTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGTGCTGCTGAAGTTGCCCGCAACAGAAAGTCGCCAACCGGTGATACCACGATATAAGGCTGAGAGTCAACGCCATGAGCGGCCTCCTGTTTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACCGCCGTTCCGGGCAACCCGACGGTCCCTGGCCACGGGACACCTTACCATACCCACGCCGAAACAAGCGCCTGCTCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGAGGCAGAATGACGATCATATCGACGTCAATTATTACCTCCACGGGAAGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCCGGTAGTCAGTAAACCGGTAAACCAGCAATGAAGACGCAAAGCGTATTCCAGCGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCTGTAAAAAAATTACGCCCCGCCCTGCCACTCATGCCGGTACTGTTGCGTAATTCGTACCAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCGGCATACCTTGTCGCACTGCGTATATGTTGCCATGGTGAAAATGGAGCGAAGAAGTTCTCCATATTGGCCACGTTTAAATCAAAACTGGTGGCAGCTCTTCCGGGGATTGGCTGGGCTGAAAAACATATTCTCAATAAACCCTTTGCAGGAAATAGGCGGTTCATATGCTGCGCCACACTCTTGCAGATATGTGTAGAAACTGCCGGGAAATCGTCATTGTTCCTCCAGAGCGATGAAAACGTTCAGTTGCTCATGGAAAACGTTCTGTCGGTGCGAACCTATCCCATATCCTGCCAGCTCACCGTCTTTCATTGCCATACGGAACTCGGATGAGGCATTCATCAGCCAGGCAAGAATGTGAATAGACAGATAAAACTTGGCAACGTTTTCTTACAGTCACAAAGCCCGTATATCCAATGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAATACGCCCGGTAGTAATCTTATTTCATTATGGTGAAAGTTGGAACCTACGTGCCGATCAGCATCTCATTTGCCAAAAGTTGGCCCAGGGCTTCCCGGTATCAACAGGGACACCAGGATTTATTTATTCTGCCTTGCGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAACTTACTGATTTGGTATGATGGTGTTTTTGAGGTGCTCCCCGGTGGCTTCTGTTTCTGGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAACGCCTAACCGTTATCCTGACACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATGTTACTTCACGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATAATACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGGGGGCCGCGGCAAAGCCGTTTTTTCCATAGGCTCCGCCCCCTGACAAACATCACGAAATCTGACAAATCAGTGGTGGCGAAACCCGACGGGACTATAAAGATACCAGGCGTTTTCCCCCTGGCAATATAATGCGCTCTCCTGTTCACCTTATTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCGGGTAAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCGGCGTACTGTTAATTGATTTAGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAAGGCGGTTTTTCATTTCAGTGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCCGAAGTGCAATTTATCTCTTCAAATGCCTTTCTGAAGTCGGCCCCATACGATATAAGTTGTAATTCTCATGTTGACAGCTTATCATCGATGAATTA &,;ADDDDB@@BCEBBCCBA******55656...59=9=;<6677:7644411111?@A@A@A@7779::8899:;;;;>:::;?@0///,+)(((),0/(213;<>>=('&&%%%%%&&(*+./3:>111**(((,->@@@CCEBBBBEGCC>==>?B>>B?88/////88000))))*DBCE8666745566?@@ABC<:;:943:;<4410//((&%$$$%&&'+,,0.-)%%%%0.-7501?@FDA-,,,-38=@.-...>88432,(''$$$$$$$%&'(*:@ADAD<;8422-****-36:<>>>?=988;>@?=>><<=<//+**,1:@?@@==???A<??@;:;972)'''(.0589B@==+***+0189;CCBAABBCA0??AC???BCABA@99<>;<1-01237=>?B=;:>A=?>?>@@?>==<1--./..0'&&&&+188;<????@@@?;=8.-&$$$%&(4478?>?>=<<;<8644.../09)'')--.489:<ABBCEABCCCDDBAB??>>?@BBABACAA>>@A>@?@,/==A>=<<<;<=>@A@<<:9880001>BBCBCF??>>>AACDDDDB@@?@A444<>?AA88888>?.--668<311+*()(%%&&'&####$&'&&()))%%%%&''&&&%'&%%%%&&&'19?@@CCCED<;;;A==995551-,'&&%&0000010--12799999;666<<54ABCDB>;55411136COMAHG{JG{IJKHHFDDDEFHGKJH{{HGARBCMKFFIIGHG{HG32222IDCC=:?86)((()'''''&('*++,*(&&&))))))*+01211.-,--*('&&'))))),-44//.2456-0:<<=?@BFFEG?>>?<>?GIM\LEGEDG,,,,-333*''''()--.8BDCAA?..,,))*)())'(())&))$$%%%%%%%&'(+'')*'&&-366611254349877744449@0?@@A15578AEDGM{H@????EA*((%%%%&'''&**+/<9B332337755356:9;?@BECCCC+*10233335BD<7,,(''(()>;2.8:?@???B:=AA><=>?22222313100145?931*('&&&()+%%%&&()+-013;<FEDDDFADC;78@ACBCD?@?@@E////0LIGGEDGHDGIEDFNF@-,,++/119+*)'&&&%%'&&%%&%%%&*....+))))'&+))+**+,-/<<52--(((//.*))*&&&&&,*++,,333356;B>ILFE=<<EDC?@<0))(''',-/,,('((()+))+**)))&'''(/0/12235>BF:97311)1*(*)&&''(()21.---)(&'&&))()*....//..*'&&')))''&&&&(+('&%%&).455+),'&+/4822-'&&&&(*''')**)))+471122/.+++(&'%%&&2312,+**+,.+))'&$$$$$%&'&&$$&&'+565233451.&&&()=@@DCBCECFIHF>>>>=>BB=>===BCAC222<732.-,,.,,11*'&&%%&''/--0..,,('*.&&&&%%%&(,,,''&$$$%%$$&%%&&&$%$%&)&'&''&'&&&'''&&'%%$%&&&+++,,,HGGEFG????>?BEHAB9999:ADBA@@BB@BBC:999>@>EFEIQFPLSKDGGHFLIJIFIKFIHKHJJGC0/=??@@FJKKGH::9:;CCEGD<@ADEACAF@???>CEDCHBEIGFFEC=B=AA{DDBDCB>;55556A8<265553,,,,+-,,-/1256?B2<A>CAAFEB??==<B=6211((&',27:;55441(('''((1--,&())-/8<34@B>;41412259=0///00-./,,+++05@AA?1110/1*(%%%%&'(10/)'&%$$%&)-38;CDGED::C=<50//58FNJ@GDEB@@ABED?ADCDCC0/.-./.+*)''())6@BCFEDCHE=)(((()-2B5422222785341100/*(%&&(&()))))/4BD6<>ADA>D?:722212=BC;::>=>>??@200002222(&&&'(+'(-02399;;;<=<<<?B>::.''&&%%%&&$###$$(%%%&'''(*/,18434-,,,-12220/.01<655556FEHGDFDDBC??>BAFBDA@??@FF:9CDGEFHHH{FEFDEA?@@AABDIGGH{OFFGC@?===?*))''&&*''&&%(*3368:<=------:;?-,,,->?A@>><9832254;;;:9877,*)))((++**,,-7D?AA?D<@@C?F;7@>BA?;-,01557C?AAA@EE+******+-&&&&&+<A0//121(''&'(/072355633469:C;<FF==603644***+-=?<76.-/(%%&%&&)-***6?A;7750//65467:0///02((&%%%&)+,/**/52///+/79420.//,))))(&&%&&++-0:=,,*)(&'&&&%%%%&/45BCBDA>70/1311134((922222<99---.781/11**)24((333445582.--.,--02)((03*((*78>AAAB@>6667;<>==>A??ACAC??==>>>?=366>C<99:?@BBC>?EGECHDEEDHIFGFFGHFIELHJFFEDB=><@)(&&'*+6;;/.4644445;;@;211123++++&$$$$%'&&'*++-.--/5'&&&&')+>??@@::989<65566>>GGIFCECBDDDFHEF@9;433320*))34:>=>>@=;;<=>D<43.../=<1111118887:;<50/+),*)**+23:74446:AADD@9989::+**+31111..)'*+)*++-1/0133)('%$$%%%-/03ACAAA@AAC@CDEECEFEBD>=44322333?BDEEGEEGEFB??CDDMIEFFDDGFCACCE=<+((*))+47<>@CCEB7//23*(((+,'&&&'&&,3589)(''(0565655520/----(((((2/06..*))%%'()*7:@AFDCBCBBBA@<;+ NM:i:270 ms:i:4320 AS:i:4260 nn:i:0 tp:A:P cm:i:257 s1:i:1768 s2:i:0 de:f:0.0706 SA:Z:pACBB_PL,1,+,73M1I2914S,26,1; rl:i:0 ru:i:0
c8444849-ddea-4bed-b1df-80b1981aac85 2048 pACBB_PL 1 26 63M1I10M2914H * 0 0 AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCCAGTGAGCCT &,;ADDDDB@@BCEBBCCBA******55656...59=9=;<6677:7644411111?@A@A@A@7779::8899 NM:i:1 ms:i:140 AS:i:140 nn:i:0 tp:A:P cm:i:7 s1:i:56 s2:i:0 de:f:0.0135 SA:Z:pACBB_PL,4292,+,112S2871M52D5S,60,270; rl:i:0 ru:i:0
5337d681-20a1-405d-9224-74596d8164d3 0 pACBB_PL 4287 60 107S25M2I125M1D111M1D42M1D2M1D119M1D29M4I1M1D2M1I74M1D20M1I3M2D43M1D65M1I64M1D62M1I81M1D45M1I428M1D118M1D33M1D104M4D446M1D102M3D182M1I18M1D128M2D95M2I11M1I75M1D4M2I63M1D122M1I46M2D10M5S * 0 0 AATTCATCCTGAACTTATCTAGACCAGGCTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCTTGAGACCTTTACACTTTACAAGTAAAAGGTCTCTTCACTTAGTGAGACGATTCTCCTTACCCGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGTGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCGATGGCACTGAAGTTGCCCGCAACAGAGAGTGGAACCAACCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCTCCTTCCGGTGAGCGCGGGGCGCGGAGAGCTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCCCAACAGTCCCCGGCCACGGGGCCTACCTGCCACCCACGCCGAAACAAGCGCCCTGCACCATTATGTTCCGGATCGCCTCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCATATCGTCAATTATTACCTCCACGGGGAGGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAACCAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACGGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACAGCCGCCCATTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCGGTATCAACAGGGACACCAGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAGCGAGGTATATACTGGCTTTATATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGATGGCTTACGAACAGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGCGGCTCCCTCGGTATACTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCGGATTCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGAAGCCATTGATTTAAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTCCTCCGGCCGTAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGAAAGTCAGCCCCATACGATATAAGTTGTAATTCTCATGTTTGACGACATCATCGATGAATTA 0:8=ABB@:::=A@@AACC=54442))*))*.67:;=6435333******8888889:?>>===:::;;=777999:?>>>?@EF@?@?@ED::6522,,,16;=?@?@2222258<><=<<;?@ABCA<<AB:71111115<AA<<<<<AAA>?>=>@@@CDB@;;:::>=9888:<<<?????@:9843214779988;=<931*))+--./,)(()05>@??C@C=<:;:;666699;@@43212755684433330*))*+.59;<><>>@A?>??@DA@@CBBFCACAA@@@@BABCA>>8==@@AABACABB@<>?>???>;;;=>FDBAA@>@@@A@??92121344457889@AA?==>>>==>0/97=AAEA<<;<426><=73237878955988982*))*%%%%'''((0579=?>@@>?6554,,,/08<???10101@@@BBAA?==;<333338;9889???AACCBA?>;>=?>;:9::;<?@@=4456;>>@A@BCCDDFCAA@@@<<<<=?@ABBBA::A:99))-,,-2:<>9+****9;8541/+('&%%'(),/???><@?A????@BAB@?>??@A@??>>@C@C@@ABA?@655555@:87;;@?=>>-,,,-:7633112659/.(%%%&+/13457222/**'$%&)/6<CC;))((+,+-.13C<AD87667;;<55553569<=(''./018:;::?;@EDFIWGHBCDEDEHGFABCCCKJHIMJFGLLE{JJ{HD{FFRM{?=>B{ICACDF=>{D@AABAIFHIJFJJJGIJLIJIMI{JJC64555GJFTHIGVIILGDGEGDI@?=6;6****588888BDFXFIBCD:9889>C@:?@CFE@CF>;421112888A@CF{K99HD?E@9,((()*,223===<?DGGFDFH{DFCCCD>65655:)))))))))))436>>@?BDGCADEDJHIIJHN{F:999:<5><<>.----DFAAAM{>=@@@<AACGJGFCACH76566BAABAB=:62122113**11134>?C@?BABEGFNIL/.../CFINEE>>6655=@@EF7)29=A;>F??CLHI{JHJEECCDCEIKIKHNIK{QODDHECMHGLFFFLEC@@??<=>?ACDFLFGGGGLCDA@?>?>?ADHJHPCGFIFIDMMIBDDBA=888899984432368868BFFFJFFELIFDBE=?AA<<<ACEIB865577,,,+06233:EDGCMJ{G{DDEGGGHLFFPPDD@AA@@AACC=BG@DED?>?97:AA*A=9666557788<>?BDKJ{JLLJLIMFGEDGGEFI{GD>>>8>@DEKEK;:::99;<?029AAHH<1111+0====LK{EH=<:==@DJDA??AA?E@B@B4337:??8AC@=;544457>222<=??A;>=;:8;;:;5BBCBD@CBDCCCBDCDE@@ADNDLCEDA@@8(''''022:==?>>>@?<98>?....---7<>DEEGFIIAFCA@@ENG?>>?>AABB7659>ACEAAA?ABCB33.-**,00226;:?CCB@>CFA@B<?@AB800126)%%$$%%$$&'('.567BFLEFCEGBDD@::;<>@?>DC>966(''+,-8:9:>??EHFFGGBJEEEB88877;==BABAB@BABDA{GCJFD<>DAACDGD@@?BABHGF{GDGB<<<<=LDC{{G32222HCEDLH{H1117:=<<;)02=<=>A87767;>FKGFEDEFF32<EGCEGEEJHECCDAD==<CE336FFJLJ>[HBCABDDFHDIGGLGEGGCGF532222129:>FHHLOFKHKHFHFHF?><@EJMFHEHFDEEAKeDGE{FH(1=ACA>?7)3176CDEED<=FECGGGDE?A@CDBB=22223BAEFFEDGHFBBA@AA>@DFFBBA?@AA@@@?????BCFFFFCCA@;;::505<<<?>9889:<;===<;<::<<>??;8=?BFGICBAABBBABAA@@AACAA@?===<=@+++5;;>?>>>@ABC7:999;;;;;==88)86679IEDC?====>=====@B@@>?>>@AB>;;;:=E?A@???AAC??BA@BAABA@AA?>==+****+,+*,--+,,-((()))7BAA@@=<<;;=>?A??>??A@BBC@@?@?ABG<<<<<=>***)*2236470./0005=A@?@?@BA@AA88888?@CDECECCBBABBCDCCG;;888:;=;<)))**-/8:<=?==>>@C@@@33333=>?>@?=;<;440.+*)'(''**,411221(((((;<<;;446667887+++-66600447@CF6555555413//5==<<2;ADD@DBBDCFDB><?E98?>>/3522445?@AC//CBMH;7688454899:DFEFEEKPJEFGDENB666I{><<<>B4..)))+4ABBAA98889CCDDDAACD;;:9999889/055/...035=>>?>,++('&&%$$&'-01;EBBDCDDEEDHEDDFFBDEDCDCCDCEEGHFFFEFFFDCGDCEC@ABC9ABAC>;:<1+++,,43D>0///&%%%&&&((1110001<ABAA@?;;:89=@BBBCCEFECB=<553232,149>111<;@AAAGIGFH===EGDVEDBCEADECFCLGOEBB87666.,(())((),0/3222339972603=ACDDECC;::99?;,,,+('&&%%%&&&''11-,,/5++++,A@BHJCLGBCFEDFCHJLDEGCG@@?@BCEEDHEAGJHIJCCDABCJ:B4333=?998;<DB?<+'&&&%$$$$(+2888766=<;CB?A@?@BCHI?N<A@==98:;::;74336<:=@BCDEDEBECEEDBA><=8/399<@CFC?CAB?==>AF@F?LBICD@;:7/)))))249B>=54,+135<C=ABCCKEBGGIFFHG@DEFHJHIFM{{HBCBFDBB????><<<=667CEDEGKCA<874234;=AAC>)((3<?BACE@?=:;<?DFEGDDJGGDHFLILFLIFIHIFE;*((&&''3=@@@@=>9;: NM:i:84 ms:i:5361 AS:i:5348 nn:i:0 tp:A:P cm:i:416 s1:i:2609 s2:i:0 de:f:0.0239 SA:Z:pACBB_PL,1,+,73M2955S,17,2; rl:i:0 ru:i:0
5337d681-20a1-405d-9224-74596d8164d3 2048 pACBB_PL 1 17 73M2955H * 0 0 AATTCATCCTGAACTTATCTAGACCAGGCTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCT 0:8=ABB@:::=A@@AACC=54442))*))*.67:;=6435333******8888889:?>>===:::;;=777 NM:i:2 ms:i:134 AS:i:134 nn:i:0 tp:A:P cm:i:7 s1:i:51 s2:i:0 de:f:0.0274 SA:Z:pACBB_PL,4287,+,107S2916M12D5S,60,84; rl:i:0 ru:i:0
11820868-051c-4c6b-ae74-aea5790dc92b 0 pACBB_PL 1 60 132M8I11M1D9M6I2M2I2M6I1M1I14M1I33M1D69M1D6M2I839M3D29M1D8M2I6M1D157M9D10M1D9M6D2M2D2M6D26M2D27M1D327M1D152M1I138M2D200M1I2M1D34M1D33M6D8M1I1M3I65M1I110M1D113M1D87M2D209M1D5M2I29M2D123M1I8M2D27M1I89M1D25M1D16M1I78M1D94M74I7M3D13M1D578M1I148M5D7M2D2M6D4M1I12M1D3M9D365M2I22M2D99M1D24M1I79M1I48M1D7M3I98M1I19M1I162M1I58M1I32M3D71M1I142M1D39M1I70M4D178M1I195M2D36M2I64M1D56M1I51M3I104M2I1M1D14M5D66M1D145M1I20M5D18M1D8M1I2M1I3M1I12M4D36M1I3M2I177M2D249M3D5M1D103M1D3M1I5M1D56M11S * 0 0 AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGCGGGCGATGAGCGCAACGCAATCGTCTCAGTGAGCCTCTAGTACATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAATCGTCTCAGCCTGTGATTTTGTTATCAATAAAAGGCCCCCCGATTTGGGAGGCCTTTTTTCGAGAAATTAGTTATCATTTTCTGGTTAACAACAGAGTAGTTAACCGGAGCAAACAGTAACCTTTACCTTCCGCCTGGATGTGACCGATACCCGGGAACGGTAAATGGGAAGCCGCGATCGGAAGCCACACCTTTCGCCGCGTCCGCGAACGCTTTTTTACGTTCAACCGCCGCAGATTTACCGTCGATGTCCAGCTGGTTGGTAACAGACGGGTCGTCGAACTGAACCGCCGCAACCAGGATCAGGTCACCCAGCAGCGCCAGTTTCTGACCCTGAGATTCAACAACGTAGGTGGTGTGACCCGGGGTGTGGCCATGGGAAGCCAGCGCTTTGATACCCGGAACCAGGTCGGTGTTACCAGAGAACGGTTTGAATTTACCCGCTTTAACGTACGGATTTAAGGAAGCCATCGCACCTTTGAAGAAACCTTTAGATTCGTCGTCCGGCGCTTTGTCCAGGTTGGTCTGAGACAGCCAGAAGTCCGCTTCTTTCTGGTCCGCACGAACAACCGCGTTCGGGAACGCCAGCTGTTCACCAACCATCAGACCACCAACGTGGTCCGGGTGCATGTGGGTGATGTAGATTTCGTCAACCTGTTCCGGCTGGTAACCCGCCGCTTTCAGGTTCGCCGCCAGACGACCCAGGGTCGGACCGAACAGACCCGCCGCACCGGTGTCAACCAGAACCAGTTTAGAACCGGTGTTAACCAGGTAACCGGTAACAGAGGTTTCCAGCGGCGCTTTCTGGAAAGATTTCGCCAGCGCAGACTGGGTTTTCGGCACCGGCTGGTTCAGACGTTTGTCAACCGGCAGCGCAACGGTACCGTCAGACAGCGCGGTGATTTCGAAGTCACCCAGCAGCATACGGTAGTAACCCGGCGCAGAGGTACGAACCTGCGGCGCCGCCGCAGACGCGTGGGTAACGAAAACCATCTGCGCCGCGGTGCACAGACCCGCCAGCGGCAGAGTTTTGGTCAGGTTACGCATCTGCTACTTTCCTGTGTGACTCTAGAAAGGCTAGCACTATACCTAGGACTGAGCTAGCCGTAAAAGGCCTTTTGAGACGATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGTCTACTTTCTAGTACATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAATCGTCTCACTTTGTGACAAGAAAAGATCCAGCCGAAGCTGGATCTTAGTTAGCCTTCTATGCCGATTTTTTAACCGATAAGCTAGTGCCGGTGGCTTAGGCCGAGCAATCGTGCAGCACCGGAGACATTTTGGTTGGCCTGTTGCATGGCTTTGCGCATCAGAGATTCCTCGATTTCATCGAGTGACAGGCCGCTGCTCAACAATTGGCTGATCCAACTGCCTTGGCCATTGCCTGGCTGAATAAGAACGCCGTCCGAAGACACCCGCTCAGAGGCGGTCTGGGGCTCTTCCGGCGCGCGTGGAAACAGCGCCTGTACGCTGATAGATTCGTTCGGATCGGTTAAGATTATACCACGCTCGATTACATTTTCTAACTCACGGATATTGCCCGGCCAGCTGTAATGCAGGCAGGCCTCCAGGCTTTATCTGAAAGGCCTAATGTTCTCTTCCCGTATTCCTGGTGGAAGCGCTGAAGAAAATGCTCAACCAGCAGAGGAATGTCTTCACGGCGTTCGCGAAGGGCTGGGATCGCCACCGGAAAAACATTCAGCCGATAATACAGATCGGCACAGAAAACGACCGGCTTTAACCGCTTCGGCCAGATCTTCGTGTGTGGCTGCTATAACCCTTACGTCTATTTTGCGCGTCCTGTTGTCACCAACTCGCTCCAGCTCTCCTTCTTGGAGCACGCGCAGCAAGCTGGCTTGAGCTCGGGCTTAACTCGATCACCTCGTCAAGAAATATAGTCCCTTTATCGGCCCGTTCAAAGCGTCCCATGCGTGATTGGGTGGCGCCGGTAAAGGCTCCTTTCTCCACGCCAAACAATTCGGACTCGATCAGGTCCGGCGGTATCGCCACACAGTTCACAGCAACAAAAGGCTCTGCGGCGCGTTTGAAGCGCCGATGCACTACGCGCGCGATGACCTCTTTGCGCACTGCAGTTTCTCAAGTAACAGCACACTAACTTTGCCCTGTGCTGCCACAATACTCCATGCGCACCGTTTGATAGGCTGGGGTCTGACCAATGCCGTAGTACTGTCATTCCTGTTTGTCTAGGTTTTGTACGCAGCGACACCAGTTGTGATTGTAACTCGTATAACTCCTCGATGATGGGGTCATTCTTAAAATACTGTTTGAAAGAGGCAACATCGTCCCATTCTTCGGCCGGTTTCCAATGACCCGACACTTATCACCTCCACAGCCGCGGCAACTTACTTCCTTAAAAATGATTTCTCTGCCCATAAAAGCAGAAGAATAGGCGCAGGCGTAGCCGAGCAGAGTCAACATACCGGATCTTGCATCTGCCCCAGATCGGTCTGACAGATTTTCACTTCAAAGGAGTCGATCCATTCCATCTCGGCATAGAAACATACATTCCTTATCGATATCAACTTCCGTAGGGCGTACTTTGACCAAACCCTTGAGCGAATGCAGCTGCGGCCCTGCGAGGAACATATCATACTCGCTGGCGTGGAGTCTAAGCTTCCTGGCCAGTTCGGCATCTTTCAGGCCTGACTGATAACCCTGTCTTAAGAAAAAGCCTTTCGCTCGTTCGATTCCCAGTGTATTGACGCATTCCGGCTTGAAAACTCGCCATTGCTGAAACCTGCAGTAAGCATTCTTTGTTCGCCAAGCCAGATTTTGCCTTCCGTGCTTTGGAAGTGAATCAGGTTAGTCAGGTCCTTAAAATCGGAATGCTGGATTTCAGGCTTATATTTTATTGGCATCTGCTATTTCTCCTCTTTCTCTAGAAAAGGCTAGCACAGTCCCTAGGACTGAGCTAGCTGTAAAAGGCGCAGTGAGACGATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGTCTAGCAGTAGACCCGACTGGAAGCGGGCAGTGAGCGCAGCGCAATGTCTCACTGCGCCTTGAAGCGTTTGCTCAAGCGGCCTTGGGCAATTGATCAAATGCTTAAAAAGCCTGCGCAAGCGCGGCTTAATTTCGCTCGCTCGATCATTCTAAAAATTAGAAACACATTGAAAAACAATACCTTGAAGTCGGTTTTCAGACCTTGGCACAGCTGTTGCACTTTGTCCTGCGCTTTAGCTGTCACCGGATGTGCTTTCCGGTCGATGAGTCCGTGAGGACGAAGCAGCCTCTACAAATAATTTTGTTTAATCTAGAGAAAGAGGAGAAATAGCAGATGCGTAAAGCTGAGAAACTGTTCACTGGTGTCGTCCCTATTCTGGTGGAACTGGATGGTGATGTCAACGGTCATAAGTTTTCCGTGCGTGGCGAGGGTGAAGGTGACGCAACTAATGGTAAACTGACGCTGAAGTTCATCTGTACTACTGGTAAACTGCCGGTACCTTGGCCGACTCTGGTAACGACGCTGACTTATGGTGTTCAGTGCTTTGCTCGTTATCCGGACCATATGAAGCAGCATGACTTCTTCAAGTCCGCCATGCCGGAAGGCTATGTGCAGGAACGCACGATTTCACTGGAGGATGACGGCACGTACAAAACGCGTGCGGAAGTGAAATTTGAAGGCGATACCCTGGTAAACCGCATTGAGCTGAAAGGCATTGACTTTAAAGAAGACGGCAATATCCTGGGCCATAAGCTGGAATACAATTTTAACAGCCACAATGTTTACATCACCGCCGATAAACAAAAAAATGGCATTAAAGCGAATTTTAAAATTCGCCACAACGTGGAGGATGGCAGCGTGCAGCTGGCTGATCACTACCAGCAAAACACTCCAATCGGTGATGGTCCCTGTTCTGCTGCCAGACAATCACTATCTGAGCACGCAAAGCGTTCTGTCTAAAGATCCGAACGAGAAACGCGATCATATGGTTCTGCTGGAGTTCGTAACCGCAGCGGGCATCACGCATGGTATGGATGAACTGTACAAATAACTAAGATCCAGCTTCGGCTGGATCTTTTCTCTGTCACTCACTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTCACTTAGTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGATTGCTGCTGAAGTTGCCCGCAACAGAGTGGAACCAACCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGTACCGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCCCAACCAGTCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCCTTTTCACCGCCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGGAGGCAGAATAAATGATCCTTATCGTCAATTATTACCTCCACGGGGAGAGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAATAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACCGACGACCGGGTCGGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCGGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAAGCCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAGCTTATTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCGGTATCAACAGGGACACCAGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACGAATTGTTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAACTTACTTTTTGGTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCATGAGGACGTCAGCGCTAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGGAAGATACTTAACAGGGTAAGGGCCGCGGCAAAGCCGTTTTCCATAAGAGCTCCCGCCCCCCTGACATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAGAGCTTCCGACAGGACTATAAAGATACCAGGCGTTTCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACGCTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTCGTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAAGTACGCTGCGAAGTCAGCCCCATACGATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCGGCGATGAATTA 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NM:i:378 ms:i:12864 AS:i:12662 nn:i:0 tp:A:P cm:i:1025 s1:i:6185 s2:i:109 de:f:0.0281 rl:i:0 ru:i:0
8b7db6e7-70c6-4a09-b37e-0de040b76a19 0 pACBB_PL 4287 60 105S10M1D85M1I120M2I212M1D107M1I343M1D46M2I10M1D365M2I108M1D21M3D2M2I3M1D2M1D167M2D81M2I64M1I1M1I318M1I55M2I2M1I109M1D105M1I106M1D11M2I6M1D22M1D180M1D77M1I119M6D48M5S * 0 0 AATTCATCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCTAGTGAGCCTTGAGACCTTTACACTTTACAAGTAAGGTCTCTTCACTTAGTGGACGATTCTCCTTGCGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCAGGCAGCGTTGAGTCCCCGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGTGCTGCTGAAGTTGCCCGCAACAGAGAGTGGAACCAGCCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCCCAACAGTCCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTGCATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCATATCGTCAATTATTACCTCCACGGGGAGAGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAATAAACCGGTAAACCAGCAATAGACGCAAGCGGCTATTTAACGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCCAGGCGTTTGGGGCACCAATAACTGCCTTAAAAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCGCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAGCTCGGATGAGCATTCATCAGGCGAACGGAAGTAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGTGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGAGATTTCCCGGTATCAGCAGGGACACCAGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCGAAAGCACCGCCAGACATCAGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACCGAGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCACGCCTGCGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAGCCGTTTTTCCATAGGCTCCGCCCCCCTGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCGGGTAGGCAGTCTTCGCTCAAGCTGGACTGTATGCACGAACCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTCCTCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGAAATTATTTTATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCGATGAATTA 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NM:i:67 ms:i:5483 AS:i:5468 nn:i:0 tp:A:P cm:i:432 s1:i:2603 s2:i:0 de:f:0.0177 SA:Z:pACBB_PL,1,+,73M2964S,22,2; rl:i:0 ru:i:0
8b7db6e7-70c6-4a09-b37e-0de040b76a19 2048 pACBB_PL 1 22 7M1D56M1I9M2964H * 0 0 AATTCATCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCTAGTGAGCCT ((((''(*'''((*,399:A???>==><<<4/.....36366888<9::;>A;:::;?A@B52+)((),,333 NM:i:2 ms:i:132 AS:i:132 nn:i:0 tp:A:P cm:i:6 s1:i:54 s2:i:0 de:f:0.027 SA:Z:pACBB_PL,4287,+,105S2927M1D5S,60,67; rl:i:0 ru:i:0
b3846fc3-30c8-488c-a0b7-b99500971507 16 pACBB_PL 4287 60 104S92M2D334M1D7M2D39M1I121M1I140M2I61M2I126M1I480M3I51M2D7M1D2M1D3M1I18M1D8M2I135M1I275M1D87M1D265M1D31M1I16M1D37M1I64M1I1M2I47M4D31M1D145M1D8M1I64M1I8M2I61M1I144M4S * 0 0 TAATTCATCCTGAACTTATCTAGACCCGACTGGAAAGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCTTGAGACCTTTACACTTTACAAGTAAGGTCTCTTCACTTAGTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTTCGGCAGCGTTGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGTGCTGCTGAAGTTGCCCGCAACAGAGAGTGGAACCAACCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCCTCCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCCCAACAGTCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCGCCCTGCACCATTATGTTCCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCATATCGTCAATTATTACCTCCACGGGGAGAGCTTCCGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAATACAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACGGTCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAAGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGACAACTTAGTTATTTTTTCTTTACGGTCTTTAAAAGGCCGTGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCGGTATCAACAGGGACACCAGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTTGCTTCGGTCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAGCGGAGGGGTACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCCTGCCCCCCTGACAAGCATCACGAAATCTGATTGCCCAAATCAGTGGTATGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGTTCGAAATATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCCGGGTAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAACCGAAAGGGATAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGGAGAACCTTCTCGAAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGAAGTCAGCCCCATACGATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCGATGAATT CCDC@????@?@?>???;6***<;<<;?2//1))))**67;==>66566@?;5.***+:7766677=76777?B@@@;44?????BCBABA@@?>>=<<=:7722.***68::7336:?<8333033::;=;=>>@A?=<=;:::;B00001A@;9621387;:45/---./04222222-'%%'%'/<;.-+''(:;:::;HCA?:87622243488)((((235688444//0<<@;;:98988-+++,B@D<:A>>;:9877::=@ABBA@@A@<ABABCCECAABDFCBBDEDGF@>===>BBBAA>>>77778BBEHEBBBABDDACBECEE>>>>?A@AA@AA@?<4399889:?@A=>88==??>;;;?:99431/,++,=A@>>>>ACBA:C777>;9::==AA@@=;<<=>>77778ED?>======<<@@?C6====?@@@??>@@@@@A@A@@11111@<;<<<?A=>==>?>:8889?@?CABBBBACB10//0D@ABA@@@;;98788>>?22222@??=8444522244=>>@<===96=?>><;;;;===<<=>?@::;+()===>??===;8;<8ABABAAA97,+)(((**--8855643655:::<:999:<?>==77777>@A>:87.+0.---.:;BAA@?>>:::::?@?@@@?@AA@A>>>>=@?>?@@=6-,,,,,-56>>A?><;76677:;@??>>@?<=<:;<==?@C@@B@?<:;::;==<<==<BA?>>>>=?>=>??>>;;=>??@=6334899974104556;<<5553?@@=>>>>?=>==?ADHJFGA0-**,-8/.,+0.+,,())(())8::ACC>>==>?CCB@@<72@@@A>=>>>AA>>>>?AAAB@@@@@BBBA??>??A?=;90**<=;<<=7@@??@977787?>??>??>>@@@ACHFBA><<<;;<==45555>>941002111338?AABB?<:795???>@><=BCBDEBCEEAACB@ABBBDCBCAAABCCCACA@A>=7610,,//0)''((<=D>?DGCCCBCEEECBDB@C>>A>@EXNLHEGFCA++++,BDIFJOEIFBBB@BCDDBBBCCFEEGKEGAL^ID{DDGJDCDCAGBBBFJLHIMGMFT{EI{QIHGJHFIDH<<<<=;;;CECIBDEHGEKGIKHFDFEFEIGFEEGCE?NILLB=:((()788<6=7:::9;9989;A=C<?=:DCDIGFDCDCBCBDCD{{PFKJHIHHIO{J{KFOHEH?>BAAAAEFFDELFD@3023///A@F?>>::;FD=?A<:A?+***+:;=H=;FKDGGFIF:D?A=@@A553255=8=<>=>FB8>{GFMLIIN{E{JGJIGEIEGLECB;233202=?;?<;:::;ACCEHHIKFB@FECDE988FB:@BCA<43345BBFXJRIGFGABDEDGGJNHLHFGC9{FDBG@@@?EGGJGFD922/0.,,,,,/6;BGHHFDBCB:511.,,,,0834A;?=/----6511-))+21100000E?>FCCCEQFDEA767546>?..-))))=?DDWGC@;92/)(((*/+,&%$%%&)+--,*)((,-02766)6786400)('&&&))--.>AB@@BADDEGEDFFFGFGKFFGHBABA@AFDDB>99889>===EDB@88368B@??:99<;667655CBEDC@DGEABCABD>8//A<;<;<ACBB?;:55678D@GGb@<7535@AB;;;;;=<875+.B>>>??FEBGDBB?A@@@GE@>=;>GKGIFAA@?>@C<=BCD@B<D@@=<=4<>ACCFABADD?EA@A88896,,8868DBA>>?CYABDEG<;;;888=9?@@=<32/,10/1111128978>:@4435656566BAA656BACBDF<@ADIDHEDJJMIIG{GJIIHHIFB@A@@DBEGJH@ABEEFDF=7...9>>?HCSN{{JIIHKIFJNKJGCCAHDGDCDFEEDEGHHBDBACDADDEFHA>=<==>;:844666669<A@983(''&%%$%%&(,+++-.6??EHCDDEFTHFEHN>===;<7;>@AAAAEDEFGFEE?<8=8?CCCDDCEFEEHGBF=65/.-*)))((+-*&'),./.-//0211113377?<;7667..28<@?@@BBB???BADEE@@?@7556:FIKMFCBECKI@DBEHDLEBABACBAAA?>>?@EFEILBBBDCIF@;55;5556;9:332234,----=<?@<988668=>==>>AGFHEEECBFDFSINKIFIF@HCBC?4KE;<*))):::D<<:7>?==BCDC=C3*****A@A@920:99:CCF=FA?EBE>F42497889744<59:...44;:9<30000A:;9798$##%**+++3+13()))@@@ABDFC>====?<::0.*(')***3?AB@?<9&&&&&&>C/////BBA?==<97312=>@>?>=1,*))+*,645****+,,:::11111:=>A8BEC22223<@?>?<>?:>KHDFEIBGIHERGFF=<:81-*('&&&%&'+/--,,,2@@==333334A>=<;:;7333=44221228962+)(&$%'''()'&''((99>BA:87779:H{HEHFCA<<<<DBCAB@<<99:::DCG000(&&&'(((4;<EFDCFCDDEIHGFFIFIGIFIAAEIFEE@>76631237555535555ABCCF{GH;;;;;DHMCBB?BEHEFDKJJH?DB?>842223??FGILISC667C;8742.-)(&&((+,,(()+34>@HF?=<=>?HFEB,++**@=<<=;=CB?:??54444<;;;>7BF88888AAABDCD2..0B64/+))&'(*,,,<><<7/'&&&',,EJHGEBATDD999:HCBFC@>>;>>@B>;9888:9:H{FICA;/.:DECBIR?CDBGFHHHEFA?743/--..--17DC>EEDDE76111BC>GCAE?EHHIHIGJJHF<77>?EICDAB>==:/----245<<=;:::<=@B<<=DECJECFDECDEDCH@@@@BCDGFAHGB<889CBABBCCILTGGEC> NM:i:68 ms:i:5472 AS:i:5460 nn:i:0 tp:A:P cm:i:445 s1:i:2663 s2:i:44 de:f:0.0187 SA:Z:pACBB_PL,1,-,1S71M2D2968S,26,2; rl:i:0 ru:i:0
b3846fc3-30c8-488c-a0b7-b99500971507 2064 pACBB_PL 1 26 1H35M2D36M2968H * 0 0 AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCT CDC@????@?@?>???;6***<;<<;?2//1))))**67;==>66566@?;5.***+:7766677=76777 NM:i:2 ms:i:135 AS:i:134 nn:i:0 tp:A:P cm:i:7 s1:i:56 s2:i:0 de:f:0.0139 SA:Z:pACBB_PL,4287,-,104S2928M4I4S,60,68; rl:i:0 ru:i:0
bb6e8f07-a2c0-4485-b535-6c41c3fed79b 0 pACBB_PL 1 60 89M3I43M8I12M1I9M6I2M2I2M6I169M1I460M1I338M2I37M3I7M1D36M2D5M4I29M1D24M1I2M1I56M1D1M3D4M1D23M2D3M9D2M5D21M2D21M1D6M1D3M3I1M1D235M1I86M1D201M1I93M2I87M1I11M2D292M1D676M1I89M1I13M3D1M3D24M2D1M4D172M3D13M1D245M1I26M1D9M2I16M1I19M2D11M1I4M1I133M2I266M1I23M1I2M2D48M1I21M4D112M2I321M1D99M1I22M4I121M1I254M1I17M1D297M2I8M2I553M2I53M4I45M1D7M1D82M3D4M3D16M1I1M1I7M1I28M1D12M3D23M2I2M1I22M1D7M1D16M1D11M1I9M1I10M3I3M2D9M1D3M1D3M2I6M2D5M1D5M1D5M1D10M1D5M2I2M2D25M1D10M4D1M2D13M1I28M1I173M1D229M1D20M3D5M1I15M2D1M2D20M3D72M2D5M2I51M5S * 0 0 AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCTCTAGTACATGCGGTGTGAGGAAATACCGCACAGATGCGTAAGGAGAATCGTCTCAGCCTGTGATTTTGTTATCAATAAAAAAGGCCCCCCGATTTGGGAGGCCTTTTTTCGAAAATTAGTTATCATTTCGGGTTAACAACAGAGTAGTTAACCGGAACGAAGCAGTAACCTTTACCTTCCGCACGGATGTGACCGATACCCGGGAACGGTAAATGGGAAGCCGCGATCAGGTAACCACCTTTCGCCGCGTCCGCGAACGCTTTTTTACGTTCAACCGCCACCAGATTTACCGTCGATGTCCAGCTGGTTGGTAACAGACGGGTCGTCGAACTGAACCGCCGCAACCAGGATCAGGTCACCCAGCAGCGCCAGTTTCTGACCCTGAGATTCAACAACGTAGGTGGTGTGACCCGGGGTGTGGCCATGGGAAACCAGCGCTTTGATACCCGGAACCAGGTCGGTGTTACCAGAGAACGGTTTGAATTTACCCGCTTTAACGTACGGATTTAAGGAAGCCATCGCACCTTTGAAGAAACCTTTAGATTCGTCGTCCGGCGCTTTGTCCAGGTTGGTCTGAGACAGCCAGAAGTCCGCTTCTTTCTGGTCCGCACGAACAACCGCGTTCAGGAACGCCAGCTGTTCACCAACCATCAGACCACCAACGTGGTCCGGGTGCATGTGGGTGATGTAGATTTCGTCAACCTGTTCCGGCTGGTAACCCGCCGCTTTCAGGTTCGCCGCCCAGACGACCCAGGGTCGGACCGAACAGACCCGCCGCACCGGTGTCAACCAGAACCAGTTTAGAACCGGTGTTAACCAGGTAACCGGTAACAGAGGTTTCCAGCGGCGCTTTCTGGAAAGATTTCGCCAGCGCAGACTGGGTTTTCGGCGCCGGCTGGTTCAGACGTTTGTCAACCGGCAGCGCAACGGTACCGTCAGACAGCGCGGTGATTTCGAAGTCACCCAGCAGCATACGGTAGTAACCCGGCGCAGAGGTACGAACCTGCGGCGCCGCCACGAACGCGTGGGTAACGAAAACCATCTGCGCCGCGGTGCACAGACCCGCCAGCGGCAGAGAGGAGTTTTGGTCAGGTTACGCATCTGCTATTTCTCCTCTTTAATCTCTAGAAAGGCTAGCACTATACCTAGGACTGAGCTAGCCGTAAGGCGTGACCTTTGAGACGATTGCGTTGCGCTCACTGCCGCTTTCCAGTCGGGTCTGTTTTCCTAAGTACATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAATCGTCTCACTTTGTATGTTTGAAGAAAAGATCCAGCCCGGCTGGATCTTAGTTAGCCTTCTATGCCGATTTTTTAACCGATAAGCTAGTACGGTCGCTCCCTGGCCGAGCAATCGTGCAGCACCGGAGACATTTTGGTTGGCCTGTTGCATGGCTTTGCGCATCAGAGATTCCTCGATTTCATCGAGTGACAGGCCGCTGCTCAACAATTGGCTGATCCAACTGCCTTGGCCATTGCCTGGCTGAATAAGAACGCCGTCCGAAGACACCCGCTCAGAGGCGGTCTGGGGCTCTTCCGGCGCGCGTGGAAACAGCGCCTGTACGCTGATAGATTCGTTCCGGATCGGTTAAGATTATACCACGCTCGATTACATTTTCTAACTCACGGATATTGCCCGGCCAGCTGTAATGCAGGCGGGCCTCCAGGCTTTATCTGAAAGGCCTAATGTTCTCTTCCCGTATTCCTGGTGGAAGCGCTGAAGAAAATGCTCAACCAGCAGAGGAATGTCTTCACGGCGTTCGCGAAGGGCTGGGATCGCCACCGGAAAAACATTCAGCCGATAATACAGATCGGCACGAAAACGACCGGCTTTAACCGCTTCGGCCAGATCTTCATGTCCGGCACCATATAACCCTTACGTCTATTTTGCGCGTCCTGTTGTCCGCAACTCGCTCCAGCTCTCCTTCTTGGAGCACGCGCAGCAAACTGGCTTGAGCTCTCCCAGGCTTAACTCGATCACCTCGTCAAGAAATATAGTCCCTTTATCGGCCCGTTCAAAGCGTCCCATGCGTGATTGGGTGGCGCCGATAAAAGGCTCCTTTCCACGCCAAACAATTCGGACTCGATCAGGTCCGGCGGTATCGCCGCACAGTTCACAGCAACAAAAGGCTCTGCGGCGCGTTTAGAGCGCAAATGCACACTACGCGCGATGACCTCTTTGCCTACCCCGGTTTCTCCAAGTAACAGCACACTAACTTTGCCCTGTGCTGCTTTGTCCATCATATTGCGCACCGTTTGATAGGCTGGGGTCTGACCAATGCCGTAGTACTGTCCTTCCTGTTTGTCTAGGTTTGTACGCAGCGACACCAGTTGTGATTGTAACTCGTATAACTCTCGATGATGGGGTCATTCTTAAAATACTGTTTGAAAGAGGCAACATCGTCCCATTCTTCGGCCAGTTTTCCAATGACCCGACACTTATCACCTCCACAGCCGCGGCAACTTACTTCCTTAAAAATGATTTCTCTGCCCATAAAAGCCGAAGAATAGGCGCAGGCGTAGCCGAGCAGAGTCCAGCATACCGGATCTTGCATCTGCCCCAGATCGGTCTGACAGATTTTCACTTCAAGAGAGTCGATCCATTCCATCTCGGCATAGAAACGCCCACATTCCTTATCGATATCAACTTCCGTAGGGCGTACTTTGACCAAACCCTTGAGCGAATGCAGCTGCGGCCCTGCGAGGAACATATCATACTCGCTGGCATTAGGTCTAAGCTTCCTGGCCAGTTCGGCATCTTTCAGGCCTGACTGATAACCCTGTCTTAAGAAAAAGCCTTTCGCTCGTTCGATTCCCAGTGTATTGACGCATTCCCGGCGAAAACTCGCCATTGCTGAAACCTGCAGTAAAAGCATTCTTTGTTCGCCAAGCCAGATTTTGCCTTCCGTGCTTTGGAAGTGAATCGGGTTAGTCAGGTCCTTAAAATCGGAATGCTGGATTTCAGGCTTATATTTTATTGGCATCTGCTACTTTCCTGTGTGACTCTAGAAAAGGCTAGCACTGTACCTAGGACTGAGCTAGCCGTCAAAGGCGCAGTGAGACGATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGTCTAGCAGTAGACCCGACTGGAAAAGCGGGCAGTGGCGCAATCGTCTCACTGCGCCTTTAACTCAAGCGGCCTTGGGCAATTGATCAAATGCTTAAAAAGCCTGCGCAAGCGCGGCTTAATTTCGCTCGCTCCATTCATTCTAAAAATTAGAAACACATTGAAAAACAATACCTTGAAGTCGGTTTTCAGACCTTGGCACAGCTGTTGCACTTTGTCCTGCGCTTTTCTAGAGAAAGAGGAGAAATAGCAGATGCGTAAAGGCGAAGAGCTGTTCACTGGTGTCGTCCCTATTCTGGTGGAACTGGATGGTGATGTCAACGGTCATAAGTTTTCCGTGCGTGGCGAGGGTGAAGGTGACGCAACTAATGGTAAACTGACGCTGAAGTTCATCTGTACTACTGGTAAACTGCCGGTACCTTGGCCGACTCTGGTAACGACGCTGACTTATGGTGTTCAGTGCTTTGCTCGTTATCCGGACCATATGAAGCAGCCGCGACACCTTTAATTCCGCCATGCCGAAGGCTATCCGTACAGGAACGCACGATTTTACTTTAAGGATGACGGCGTACAAAACGCCGTGCCGGAAGTGAAATTTGAAGGCGATACCCTGGTAAACCGCATTGAGCTGAAAGGCATTGACTTTAAAGAAGACGGCAATATCCTGGGCCATAAGCTGGAATACAATTTTAACAGCCACAATGTTTACATCACCGCCACGATAAACAAAAAAATGGCATTAAAGCGAATTTTAAAATTCGCCACAACGTGGAGGATGGCAGCGTGCAGCTGGCTGATCACTACCAGCAAAACACTCCAATCGGTGATGGTCCTGTTCTGCTGCCAGACAATCACTATCTGAGCACGCAAAGCGTTCTGTCTAAAGATCCGAACGAGAAACGCGATCATATGGTTCTGCTGGAGTTCGTAACCGCAGCGGGCATCACGCATGGTATGGATGAACTGTACAAATAACTAATTTTCGAAAAAAGGCCTCCCAAATCGGGGGCGCTTTTTATTGATAACAAAATCACTCACTGAGACGATTCTCCTTACGCATCCTGTGCGGTATTTCACACCGCACTAGTCACTTAGTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCGGGCAGCGTTGGGTCCTGGCCACGGAAGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGTGCTGCTGAAGTTGCCCGCAACAGAGAGTGGAACCAACCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCGGCGCGCCAACAGTCCCCCGGCCACGGGGCCTGCCTGCCACCATACCCACGCCGAAACAAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCATATCGTCAATTATTACCTCCACGGGGAGAGCCTGAGCAAACTGGCCTCAGGCATTTGAAGAGCACACGGTCACACTGCTTCCGGTAGTCAATAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCGCAATAACTGCCTTAAAAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCCTGCCGTAGCTTACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCGGTATCAACAGGGACACCAGGATTTATTTATTCTGCGAGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCGCACTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCAGTGGCTATGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAACGCTGAAGACACTGGCTTACTATGCTCTGGCACTGGCTGGGGGTGTCGGTGCGATGCTTCATGCGCCGGAGAAAAGATGCACCGGTGCGTCTGACGAAACCAGCGTGATACAGGATATATTCCGCTCCTCGCCACTGACTCGCTACGCCCGTCGTTCGAGCTGCGGCAACGCGGAAATGGCCCCTTGAACGAGGCGAGTTTCACCCGGAATGCCGGAAGGCCTTGCTCGGAAGTAGAGGCTGCCGGCAAAGCCTGATCACCGCAGGCTCGCCCCGGTGGTTACGAAATCTGACCGCTCAAATCAGTAGTGGCGAAACCCGACCAGGACCGCAAAGATACCAGGCGTTTCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCAGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCACGAACCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAACCGCCCTGCAAGGCGGTTTCGTTTTTTAAAACAAAAGTGCGCAGACCAAAACGATCTCAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGGTCAGCCCCCCATACGATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCGATGAATTA 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NM:i:330 ms:i:12736 AS:i:12630 nn:i:0 tp:A:P cm:i:1005 s1:i:5984 s2:i:99 de:f:0.0319 rl:i:0 ru:i:0
a91040bf-a1de-40b4-8e89-d3bc6c86dc6f 4 * 0 0 * * 0 0 TTGTACTTCGTTCAGTTACGTATTGCTAAGGTTAACGCAAAGACACCAAAACCAGCACTATTTACTTTATTACGAGTGCAGCTATATATTAAGCTAACAAAAATGCCAATAAAGTAAATAAAAAAAGCATTACCTGACGAATATATAGCGCCCCGAATTTAAAGGTATGAGCGGAGCAGGTGCTATAGAAGTAGATAAAAATCTGACCTTCAGGATTCGCGGATTAAATAACATTCATGTCCTTGACTGCTTTATTCGTGTTGATGGAACCAGCTGATGGCGTTGTCGACTTTGGTAAAATAAATTCCCGAACAATTAAAAATACCAGCGCGGAATTGAGACGTTTAGCGTAGTCATGACCAAAGATCCGGGTGCGGCTAAACAGTTTAATATTTTAGGAGTTTTTTATTTACTTCTGCTTGTTTTAGCTAAAGCAATAGCTGCACTCGTAC '''(45520///61////-+++++66..-.049;88('''(**+)(&%%(&'('%%&'(**+*&&&&')/00100000066656;87/.*)('().555788JC?99999?=:+++++2><;//.-*((&%%',,///((((()76422112331.---./41(4479:;<;89322/.../0022/----020//5=>B?<@76666:;>86689<=@?@>@BECJKDGCA:>@;<=>>>1000126+''&&%%%%$$##$$$('&&)8?@88777<77776889:<<<:;:8544489???>?AB@@:?>>===?AAAABB?=<98976-+**,,,,*+++++*+3456>?>>77778>>>60100/035:;</++'&%%%$$&,.+99?BCFE?4100123<;12:<=::65,*'%%%%&)*,445444334664455633+****&&& rl:i:0 ru:i:0
139107cf-6440-4422-a923-6133588b2d94 0 pACBB_PL 4290 60 98S195M1D7M2I1M1I12M1D26M2I56M1D2M1I8M2D1M1D17M1D16M1D71M1I5M1D20M2D105M2D19M3D1M1D28M2D90M1I12M1D14M1D4M1D37M3D2M2D79M1I2M1D36M1I28M1I32M3D93M1D24M1I1M1I80M2I4M3I3M1I160M1I12M1I8M1I7M1D50M1D41M1D25M1D17M1I37M1D73M3I10M1D8M1D122M2I19M2D18M2D6M2I5M3D12M1D25M2D8M1I104M1I42M1I11M1D73M1I9M1I25M1I31M1I43M3D34M2D26M1D16M1D32M1D53M3D6M1I129M1D1M1D10M3D4M5I99M1I58M2D76M2I37M1I140M11S * 0 0 GAACTTATCTAGACCCGACTGGGAAAGCGGGCGGTAGGCATAACGCAATCGTCTCGAGTGAGCCTTGAGACCTTTTACTTTACAAGTAAGGTCTCTTCCTTAGTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTACGGCTCAGGCAGCGTTGGGTCCTGGCCACCAGTGCGCATGATCATGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGGGCAACTTTATTAGGCGACTGCTGCTAAAAACGTCTGCGACCTGAGCAACAACGCTTGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTCGATAACACTGGTGCCCGCAACAGGGGGTGAACCAACCGGTGATATACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACACTTTGCCGGTGACTCCTTCGGATGGGCAGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCCCAACAGTCCCCCGGCCACGGGGCCTGCCTGTACCCACGCCGAAACAGCCTGCACCATTATGTTCCGGATCTGCATCATGGTGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGAGGCAGAATAAATAAATCATATAATCGTTATTACCTCCACGGGAAGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACGTTACTGCTTCCGGTAGTCAATAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACAAACTGACGGGTCAGATTTGCTTTCGAATTTCTGCCATTCATCACCCAGCCCATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACTGAATCGCCAGCGGCATCGGCACACGCTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAACCCCTGAAAGTGCGACCTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCCAGTTTGCTCATATGAAAGCGAACATAACAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAACAAGGCCGGATAAAACTTGTGCTTATTTTCTTTACGGTCTTTAAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATGGTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTCGAATGCTCTCCAGTGATTTTTCCTCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCATAAAAGTTGGCCCGGGGCTTCAGTATCAGCAGGGACACGGATTTCGGCCCATGCGAAGTGATCTCCGTCACAGGTATTTATTCGGCGCAGGCCGTCAGGGTGATGCTACCAACTTACTGATTTAGTGTATGATGAATTGTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGAGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAGCCGGAGTGTATATGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGTGGCAGGAGAAAAAAGGCTGCACCGAGTGCGTCAGCCAGAATATGTGATACAGGATATATTCCCGCTTCCTCGCTCACTGACTCGCCACGCTCAGTTAGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACAGGGCGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGAAGTGAGAGGGCCGCGGCAAAATCGTTTTCCATAGGCTCCGCCCCCTGACCAACATCACGAAATCTGACGCTCAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCGGGCGTTTCCCCTGGCTCCACTCGTGCACTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATGCAGACACCCCGTTTTCGAACAAACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGGGATTAGTCTTGAGGTAACGCAGCAGTTAAGGCTAAACTGAAAGGACAAGTTTTGGTGACTGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTTTTCGTTTTCGAAACAGAAGATTACGCGCAGACCAAAAACGATCTCAAGAAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGAAGTCAGCCCCATACGATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCATTAAATTGAA **++55<>AC;:::;;CBAAB5((.1-44255+++3)))(&&%&'12<>EGGF@=*&&&'+246699998:1111/////3//.--0521048;?CD=((((3234345558AIGGGMDKB6612334CDCA??@CCFC87.**))'(()+66*)))*89744)))))4/)('&&()(((((78889?87778<;:@<,+*''&'(,**+,--+'&&&'./7;=@A@BA@@7444*)-6667:<=@8854510100643.-+++,,-.....67?BC@E@A?;;;==;;0'&&%$$$%'(*+'())))..22-+*'&&&'+,/-))))-./+((('()*+0.+&%$$$%%&&%%%%')((()*.388;CFB@@@>@;8;?AD:99@@A?<:9887787')((()/,,&%%%$%%&&87:>::44))&&&&%%&798::.*)(*/-(((()888211//0,*))''((('(@?????BAB,,,,.?@@BCCBAB@A@DDB@@@:::::@@A;,&&%%%%&&''()-**''((((787--,'&&&'%&'():>>98111;=?>766-,3569:;;<<99899<;==>>>@==;<<=>BA21////38:;;:<<:66(''''*)))++/077;?AA<?CA?////02'&&&&&$$$$%'()*4/.236,'''&&')(()).56:CHC<;;>@=221/.1&%%%%&,---,,*,+)+--2>IOF::::;EHEDDB?999EGKJEEGJLFFKRFGFJACCBCCD>BE555568ECA>.733110116-,*(''''&%%%$%%%$$$%%''(+./7*))(+),**+1531011--+++59<@@@B@>55>00-,-/1-,&%%%%$$*002A>?D><;;...=EFFDB=<<<>BG854457AAAFAB@999:ADB...--2;;210('*.'&&)/42&%%%&&''''&*,*****,32688/++++-.8;<<7*()((**'&%%%%%&&%(),222355<,,,,,,2248<=CCEIHJCIGD?98C>A>=999;66678;=>=@=:9-::9<=J7>EJA?DD?;?><.-.-.99:;>EKMJJIKNKH{EG?GCEG74487<<AADDKIKDEE****+IA=;<===<=420-,-('(,,,89ABIB94522233744411)((**++(&&'(+,.6ADEEEEEKIHEFCHECA?>>>=EC@ABB?@8767212268<@><11111FCABAA???8231/1*))(2+'('&%$$$%$$%%%%(-231/15438@;;;;>=;9;7:?@FEABDC{LHHH@?@EEECDEGJ{?>><57645EDDC55>=<<@GB@?==>@AA?>?@;::97EBB?>>><>?+,6<<=?@A@CBCCC=<<<=A?=<<;;=?=>??AEAA@></./..../:=ABHK>><:5*)**:4-..-)'&%$$%%$%%$$$$%%%%'&%$&+012;<?>??BDC;:==@JMEDECEFGFMHIHFIF765222)('&&%%',,-/47DAE@?@@AE55544888@@CA>A?E{EA?9844234==99=?AHFEHK{EE:((''')3;D5??DEHFKFHFGEEGACAA?B=@DFDDBDAD<;;;;BA@77778E@??>:-)''*+&(**,+++,--.767689<<>CBCDDJZLJ{IEGHHDECBCBCECBD>>><=C@<<=7//-((&%###%&()*,,(()))045,(('&&(()4/+***,2?AA00000?<<??>BBBA@/ABGFB:>..-----7:0//((-...5667300+*+++3BBA?@AD<>=669<==GCHGIFF{BA>;::<=>C@A>==>>DCABEBDH620('&&%'067<=>=85'&%%''''&''(4+))))))-376)'$$('('&&&&'(''%%%%&&'&('&&&*/6:::<<=ABCFHE@/..(''&%%%%&''''''-//0//,,.+*,+,-58<?BCG;:::9311101..//004@'0<922;;?32248>?>?>@BAB216779744557?>>>=>==BEE@@?>?>>>@@>=;('''(2;;;ECGA@?>>?ABA;?????A??B@@>>?:9843)))'&'()))*77)&&%%),-../=?BDEBA@>>>>>?@?@>6>??55566:9;<>>?@AAA>000,++*()),B>:1/.-''&%%&%$$%&&'''())*)**-,--.//19:4+++1<;.....**-;=?DCCB@@@>>>=>>?@886((&&))%$$%%&'''*03677>@@???=:11///03@BBCDBCBC*)))*/--04<9789:+''(0921350,-...------((&&),.1200042899211963+)(''(:;A8***)))**.::<:9777:81,))(()((()+/);3222//..))'&*+4559?332223<?@A::32234KIJOGHFEHEE<1100012.-1700.//'*(%$%%%%&&$%%%%(**.4;B<:77766??:999;=?BGDFFDECBCGDBBBEDDDCIDA=;;778-,/>>=777>>99<=?D>@HBEB?111>>733333'&&())**,???76669;<=?11,,,,++&%%&&&%&&'()*(('&$$$%%'+,/CDDBCCDFDG{KGFHDFEGFFIFFGCCB?>?A?@B@B@?@@@B?ECECCEBBECCA?AAA@AEHKDRGGEGDDBB??;53334347:777.+*,-,,,/228:*(&%$$$#$%%((*++.000-)(+,0//00=<7@>=:755787;2122:7-,''0231/04:A>>=>::333---;<9,)(*+//3244367@<<<<=>?@EIB>=:<@>3333:DBEABC/.;9955<?6CE>?<9?@;7+**+,+,,2346E>@=>0/0//8889;A=B=ABFED:000123?A900CBDCCJJGM.-,,16>798:;7/-(&')7:4)((((../@@>@BA@?@EBDGDFPGBBAA@BA<;;>@544449=;;;89:;@><<<?@ADCCCFDGEDGIKJDFB;;::;AFA((('&&&('''%%% NM:i:214 ms:i:4609 AS:i:4574 nn:i:0 tp:A:P cm:i:315 s1:i:2073 s2:i:44 de:f:0.0601 rl:i:0 ru:i:0
dd79fada-ad4d-4023-b244-d7f54f9fd87a 0 pACBB_PL 4295 60 111S17M1I76M2I175M1I15M1I10M1D25M1D2M1D34M1I63M1D31M1D1M2D7M2I52M1I2M1I2M1D60M1I83M1I35M1I44M2I57M3I32M1I86M1I32M2D13M1I4M2I140M1D7M1I179M1D132M2D11M2D7M5D280M1D12M1I99M1D50M3D141M2D9M1D188M2D15M1D81M2I124M1D22M1D154M1I20M3I6M1D121M1I84M2I36M * 0 0 TAATTCATCCTGAACTTATCTGAACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCTTGAGACCTTCCACTTCTGCGTAAGGTCGCCTGGCAGATGAGACGATTCTCCTTACCACATCTGTGCGGTATTTCACACCGCATGTACTGGTTAACTTCAGGACCTGCGGCTCGGGCAGCGTTGGGTCACGGCCCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGAGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAAGTCTGGAAACGCGGGAAGTCCCCACGATATACTGAAGTTGCCCGCAACGAAGTGGAGCCAACCGGTGATACCACGATACTATGAGCTGAGAGTCAACGCCGCAGGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGCATAATCGTCGCCCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCTTGTCGCCAACAGTCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCGCCCTGCATTCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCGCTATCGTCAATTATTACCTCCACGGGGAGAGCCTGAGCAAACTGCAACCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAATAAACCGGTAAAAAACCAGCAATAGACATAAGCGGCTATTTAACTGACCCTGCCCTGAACCGACGACCGGGTCGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAAATTACGCCCGCTCCCACTGCCACTCATCGCAGTACTGTTGTAATTCGTTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGCGAAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAAATAGGCGAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCCTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACCGTCTTTCATTGCCATACGGAACTCCGGATGAGCATTCATCAGGCGGGCAAATGTGAATGAGCCGGATTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAACAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAGTTGGCCCAGGGGCTTCCCGGTATCAGCAGGGACACCAGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACGGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCACCAACTTGCTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCTTCATGGCAGGAGAAAAAGGCTGCACCGGTGCGTCGGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAAGATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGTTTCCATAGGCTCCGCCCCCTGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTTCCCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCCGGGTGAGCAGTTCGCTTAAGCTGGACTGTATGCACGAACCCCCGTTCAGTCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGAGTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAAAGGGACAAGTTTTGGTGACTGCATAGCTCCTCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCTCAGGGAACCTTCGAAAAACCGCCCTGCAAGGCGGTTTTTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAGAGATCATCTTATTAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTATCTCTTCAAATGTAGCACCTGAAGTCAGCCCCATACACGATATAAGTTGTAATTCTCATGTTTGACAGCTTA 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NM:i:104 ms:i:5236 AS:i:5216 nn:i:0 tp:A:P cm:i:376 s1:i:2394 s2:i:0 de:f:0.0281 SA:Z:pACBB_PL,1,+,1S73M2947S,4,2; rl:i:0 ru:i:0
dd79fada-ad4d-4023-b244-d7f54f9fd87a 2048 pACBB_PL 1 4 1H73M2947H * 0 0 AATTCATCCTGAACTTATCTGAACCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCAGTGAGCCT =>???655>>?@@@?????5111111;<<>>>>60++++,34799;:89<???<<<<<=<<<<=/////;865 NM:i:2 ms:i:134 AS:i:134 nn:i:0 tp:A:P cm:i:6 s1:i:43 s2:i:0 de:f:0.0274 SA:Z:pACBB_PL,4295,+,111S2910M1D,60,104; rl:i:0 ru:i:0
b01d11eb-419c-4cb1-bc5e-7752a1591d1c 16 pACBB_PL 3174 60 523S32M1D77M1I3M3I2M1D4M1D9M1I129M3D13M1D427M1D21M2D23M1D21M1D58M1D176M2I18M1D7M1D502M1I4M1D34M3I41M2I10M1D3M1D7M2I2M4D18M2D2M2D32M1D4M2I2M3I330M1I38M2D63M1D3M1I188M1D334M1I229M2I77M1I4M1D3M1I85M2I18M3D22M1D50M1D73M4I58M2D22M3D15M1D6M2I44M1D45M3I24M1I6M1D37M1D92M1D71M1D14M1D39M1I41M2D2M1I60M2I3M1I11M1D8M1I2M2I70M1D2M1D38M1D2M1D75M4S * 0 0 TGGCGCCGGCTGGTTCGTATCGGTTTGTCAACCGGCAGCGCAACGGTACCGTCAGACAGCGCGGTGATTTCGAAGTCACCCAGCAGCATACGGTAGTAACCCGGCGCAGAGGTACGAACCTGCGGTGCCGCCGCAGCACGCGTGGGTAACGAAAACCATCTGCGCCGTGGTGCACAGACCTGCCAGCAGCAGAGAGGTTTTGGTCAGGTTACGCATCTGCTACTTTCCTGTGTGACTCTAGATTAAACAAAAATTATTTGTAGAGGCTGTTTCGTCCTCACGGACTCATCAGACCGGAAAGCACATCCGGTGACAGCTAAAGGCTAGCATTGTACCTAGGACTGAGCTAGCCATAAAAGGCCTTTTGAGACGATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGTCTACTTTCTAGTACATGCGGTAACGCACAGATGCGTAAGGAGAATCGTCTCACTTTGTGAAGAGACCTTACTTGTAAAGTGTAGCACTAAGGCGAAGATACAAAGAAGCCACGTTCGCTTTCCAGTCGGGTCTAGCAGTAGACCTTATCGAAAGCGGGCAGTGAGCGCAACGCAATCGTCTCGGCGGGCTCTGAGCATTTGCTCAAGCGGCCTTGGGCAATTGATTCAGTCAAGCTTAAAAGCCCGAGGCAAGCGCGGCTTAATTTCGCTCGCTCCGATCATTCTAAAAATTAGAAACACATTGAAAAACAATACCTTGAAGTCGGTTTTCAGACCTTGGCACAGCTGTTGCACTTTGTCCTGCGCTTTTCTAGAGAAAGAGGAGAAATAGCAGATGCGTAAAGGCGAAGAGCTGTTCACTGGTGTCGTCCCTATTCTGGTGGAACTGGATGGTGATGTCAACGGTCATAAGTTTTCCGTGCGTGGCGAGGGTGAAGGTGACGCAACTAATGGTAAACTGACGCTGAAGTTCATCTGTACTACTGGTAAACTGCCGGTACCTTGGCCGACTCTGGTAACGACGCTGACTTATGGTGTTCAGTGCTTTGCTCGTTATCCGGACCATATGAAGCAGCATGACTTCTTCAAGTCCGCCATGCCGGAAGGCTATGTGCAGGAACGCACGATTTCCTTTAAGGATGACGGCACGTACAAAACGCGTGCGGAAGTGAAATTTGAAGGCGATACCCTGGTAAACCGCATTGAGCTGAAAGGCATTGACTTTAAAGAAGACGGCAATATCCTGGGCCATAAGCTGAATACAATTTTAACAGCCACCGTTTACATCACCGCCGATAAACAAAAAATGGCATTAAAGCGAATTTAAAATTCGCCACAACGTGGAGGATGGCAGCGTGCAGCTGGCTGATCACTACCAGCAAACACTCCAATCGGTGATGGTCCTGTTCTGCCGCTAGACAATCACTATCTGAGCACGCAAAGCGTTCTGTCTAAAGATCCGAACGAGAAACGCGATCATATGGTTCTGCTGGAGTTCGTAACCGCAGCGGGCATCACGCATGGTATGGATGAACTGTACAAATAACTAATTTTCGGAAAAAAGGCCTCCCAAATCGGGGGCCTTTTTATTGATAACAAAATCACTCACTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTCACTTAGTGAGACGATTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATGTACTAGTTAACTTCAGGACCTGCAGCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCCCCTACGTGCTGCTGAAGTTGCCCGCAACAGAGAGTGGAACCAACCGGTGATACCACGATACTATGACTGAGAGTCAACGCCATGAGCGGCCTCATTTCTTATTCTGAGTTACAACAGTCCGCACCAGCTGCCGGTAGCTCCTTCCGGTGGGCGCGGGGCATGACTATTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACCTTCGTAGGACAGAGCGGCAGCCTGCCAGTCCCCCGGCCACGGGCTCACCATACCCACGCCGAAACAAGCGCCTGGCAAATTCAATAGCGGTCTCGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTAACCGTTTTTATCAGGCTCTGGGAGGCAGAATAAATGATCATATCGTCAATTATTACCTCCACGGGGAGAGCCTGAGCAAACTGGCCTCAGGCATTTGAGAAGCACACGGTCACACTGCTTCCGGTAGTCAATAAACCGGTAAACCAGCAATAGACATAAGCGGCTATTTAACGACCCTGCCCTGAACTGACGACCGGGTCGAATTTGCTTTCGAATTTCTGCCATTCATCCGCTTATTATCACTTATTCAGGCGTAGCAACCAGGCGTTTAAGGGCACCAATAACTGCCTTAAAAAATACGCCCCGCCCTGCCACTCATCGCAGTACTGTTGTAATTCATTAAGCATTCTGCCGACATGGTGCTCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATCAGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAATGGGGGCGAAGAAGTTGTCCATATTGGCCACGTTTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGAAATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTATTCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCACCAGCTCACTGTCTTTCATTGCCATACGGAACTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGCCGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAGGTACATTGAGCAACTGACTGAAATGCTCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATCCAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGATCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCGATCAACGTCTCATTTTCGCCAAAAGTTGGCCCAGGGCTTCCCGGTATCAACAGGGACACCAGGGGATTTATTTATTCTGCGAAGTGATCTTCCGTCACAGGTATTTATTCGGCGCAAAGTGCGTCGGGTGATGCTGCCAATCGCATCATTTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTATGCGTAACGGCAAAAGCACCGGACATCAGCGCTAGCGGAGGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGAAGTGCCTATGTGGCAGGAGAAAAAAGGCTGCACCGGTGCGTCAGCAGAATATGTGATACAGGATATATTCCGCTTCCTCGCTCTCTCACTGACTCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGGCTGGCGAACGGTGGAGATTTCCTGGAAGATGGAAAGATACTTAACAGGAAGTGCGAGAGGGCCGCGGCAAAGCCGTTTTTCCATAGGCTCCGCCCCCCGACAAGCATCACGAAATCTGACGCTCAAATCAGTGGTGGCGAAACCTGCCGACAGGACGAGGAAGATGCCCGTGCGTTTCCCTGGCGGCTCCCTCGTGCGCTCTCCTGTTCCTGCCTTCGGTTTACCGGTGTCATTCCGCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACTCAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGACTGTATGCACGAACCCCCCGTTCAGTCTGACCGCTGCGCCTTATCCGGTAACTACCGTCTTGAGTCCAACCGGAAAGACATGCAAAGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGGAGTTAGTCTGGAAGTCATGCGCCGGTTAAGGCTAAACTGAGCGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTACCTCGGTTCAAAGAGTTGGTAGCCTTCATGAGAACCTTCGAAAACCGCTCCGGTGCAAGGCGGTTTTTTCGTTTTCAGAGCAAGAGATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCCACAATCAGATAAAATATTTCAAGATTTCAGTGCAATTTACTTTCAAATGTAGCACCTGAAGTCAGCCCCATACGATATAAGTTGTAATTCTCATGTTTGACAGCTTATCATCGATGAATT &2348333,*)'&'''((*('(**56<>:::9:?@76DDA@?===88889@@@BABA?@>==@@CCB<444@????=<;;:8:DBA@?777<=>?>?=;;>===;;<;2((('(+:77553//1.-//0><:54*)))0///,--'''')31:::>99888<<76644<<::::;;*****?>A????@>52=<>?>@<<==?=77><;;;;<>>;54445:89789::@A@A=<=;:;;=;<3@@8429:91.,'***./55//)((('(*,//1//0/----.28?::897778855446><=;;:9:::;::98<<=;:100;==>>;755556;<=<<<;455555556638989<?7:75577799;99999:88779::::::;;;=<:;44>>><6444311+,011:9974%&'(((&'%%%%%(**+,89999<<==<AB@@?<::9:;><;<;=>>@:::88932876:>;;7:<87(''&$$%')**&%%&&%$###$$$$%'(**///--.-+)/3;@>?>?>@>>=>=;<;<<<-+'&$$#$%')+,-0)9988888;8889:>>;;;;;;75)('&&'&&&*+-/1:;<<B>>=;9987888:;775..*))'''&&&$$$$$$%'(/0468:5'''''---::AA?>::::7550/00.---+*+++4::=?=<==4.,<?@>>>>;<;;;=:/0/..???@@:9885588878:;<?BDE<;:755./66444:9<:;:;;:883,-;;)((((;?CDC855568ACA<:7778=/++)(),,9@<865577;;999:;=<;<=@BB=<;;<;<;87779=<>AHDEA98778@CAABBB=<<==????=>><<=<<==;===<@?>??>==><<=>;:889::@:9999;;;;=<==>@>==>>?>>766:667747766<=;;87766779?0//0098878>==<98889<:9644677>@?A;:999<==66687888765<===9:=>?BCB????@ADFC?=;<;>==>D???<<98;;:878<<<<>=@>>>?<====CD?@7325)&'''(559>BCGBA>==<=>??>B=CDA?>><===BBA@@?====<?>@AEC@>=:9??B@EB@@?>@PGFEDIEB@B>>>@>===98794A<<8;??@@ACC@@AFC<982+))))()-79?EDFFEDC@@A?BBA=>AA=ACCEGJC@;::<CGF:::::;<GBDIDD-,,,,,?ACDGGGGEH:::::EGGEMHC@B;50'')))34*986779<(66KED?@CCG>?>>>@?A@AGMHIC@???BGK{HIA@>@222--/B>=988978@A:<?@600009:=DGIDGA2000/-++,,-*(((&%%%&4@BBHFIHFJGHDF{I9998?CFEKIHKIF>?>:::=<43'''''9/./CB?C@?;*)((((+.013212;=CDBFDCBBBCBDGEEFFGHCAAAACDRJJIOKREFDGHFCISKHI{IJHFDECEEAA9896+)1/..068==210/-*(()+7DB>ABB63325BA76777CLFGE8:7:1.,,++,/8888KFCA000//.0--8<<<?87888<<IHMEPCFPGJGIBCC<<<;))))*::>EFJMLGJ{IKS{{HKFCBDB<;54599@@AEBB;;;<<@@ADGIGKKMB;:312228?C767555999:@@@??D@?>>?CCEGGED<<;<<;?;7222DEDFBD==<<<EBADAA>@==>/////BABBDJGLFFHEEGB@?@>BFBA>?327677<>>?BDGFGDKKGHPIFDABEIFHHG{D@IFFD@=3/-)(()*258EGHEEICCBAAFA99:2++++,66:::::=<<>>=<=::>CC@>>7766;:::;<=@A>====@@=;.----B776555:BDA@;;;BAB>>@?===8755689<==::88;=@@???@?@A>>===>?A???>>@?>>>>?@C7546556::9778:+****33;;;=====1---/C=@>44444@@A@?ABA?;//.4/../,,,+,-,((%%%%$%%''))*.345>=>@?B99?>A@:4,,,../.(((,097-,,,ABA@@???<;;;;>@@B====:=5,+++6>?DEFC>--00..050,,,-/))****-,)(&''&'..3200//037<=<4+)***''))*4@??==+'>>??<BCBBBA@534/.---010+(('&&%$$&'''(-@ECD@DCCFFGEFG>:::9<E?=<:/.../BCJFEFFIDCBA@443335ACEF@>6656:86778:889;>;>><<?4/0..//,.AAFCEDEBFIBB77:{EIPQHGFGH>>>??MIB>:::;C>:32;?B=7*(&%&((()3556=88=>>FEIH{MJFDMD<<7744449;;<<.--,,/0067>A:;<<67776JCSDFGGFGCDG?87;<777?988>>?>K?HEKIKGEFGDCBAAA?<>?@B65556CKB{O{EFAERGQ;+B=:BEHMDJLEBAAADBD854434998877;;===<;/,,-?<A>3355464444:?>43333FGGC?@?@76777C..--/02//55:@;++,:>984778?@@BAHCFEEDDIKIMLGPIFGII{EC?@CC?4343346511221111.-+'''&&&&&0:<A>7EGEEEJENDCCBG76667HJFHFEGGFJJHIJGSUFCA?==BCD333333@CBCEFTNRGAFBFA66556;;=>:AB?>>::;;;@AA0///06@BDDEF=<<<----,--.>ADBFG777664777877776,,+++++<:>?<>?>>AB@??@>CB?><<<<>@@BBDF@FA<D8*)(%%(*9<<:8554111///10---.==EEFDEIFHEC<87HGKGIOGGIHA<<<441/-.---0078EEDFEB@65556;;;<;>@@@BNDB@@?45563677:;;<7775*))))////{JEFEDBFFFHFADB:853;<EA<<<<;BCB=000011<;443/''''(<4/0?:::::ACDIEJHDDB>>>?@CKFMGHEHEJKGDEAACA66/,-4((-./;=@EDEHBAAJDEDE{ECDEBBECBEB@@ACGF<==66;'''')-*451//B?@A54445{HKEDDDB>>>DB?<<>>77778?=45;>?B@--,.-+*++-++++,D@>)(('(6<<<431244@46AACABEDBD@B@AD@@AGOQDHDCE@><<<==CDAB?:899DFQ{GQC??<?D:IHDBAB?<55<<A=<===>23:655667=>DB.-,,+*-44==<=?>CDCBEDDEE89999:@EBC9:---.=@DEDEEE@>?AB<<?0**+3236:ECAFBGEFEDFEG@I;DDECA005:57644000155558;;40000001LK{T{HAMHHFA?A2+,,DHGFM{BE@@?;20*))****+CCD?DEAEIEF@54667@CCA;;;<JF2*'??><885532268:>40/,,,(''&&'&&&'*73=@3111=<BACDCCC;@6:?>;75&&&&&((((.0:851.-.00:,,,,=;;=<=84=A00000;>?@BI99899@8/(54/)(('(((*357756877A?@6+(447BA@>740744344++.---00334450/.,))))*-7553('')2?DB;:5666677788:86******38??BAD@AADFKHIE88889?>??@A@@??@CKBAAAABBB@BCBAB@@@A?>=:99:;>:::;86446.+*('')+(((()1---:;;<98898>>??<<4438664457988878999;22,)''''%&&$$&&'.=?@;8++/./1?<9&&&&')57=?<=88888.-31,*((((11,&))((*++-..322666BDD;9/+++-1565../8/-))))ABDD@>:98)))>:::222A??>?ABDECDDAB::9443202&%&%%''(/.-'&&&%%%'(-)&%&&&&'))610.,)69::>B@?@A<;;;;>IBBA78600889D?>><;;()<@>>CC@??=7111156AD<33334>?CBAFCI{FFDDCCHDB>=<>?EHE<<<<;EB@?CDFD=@<97797677<@@CC=<5+))(''''+43224446;;=><<:820002:=<1'&&'''(''&%%$$&&'(*6:66743*'%&&'*44449AA?9,,()-.;@AAB@=41,*&*+/66879999<==>EFGF@?>>?LHDECCB?9,+++3)*AB>??@>643430//.....;<@BCADSEEEBKC>AB4103222750-,--)'''*(++++.*))):333444;;>@@>0++******,+/5;><;998-'&&%%$&&&(;<;9.,++.23/777)((&&&&&&(4489====1/,,,-179:;ADDBA@AAEGEJFIE??;<BCCAA@@AAEBB@?=567777?>8422*(&&&&&,,,.5?>?=<>>>666==>>>?>==<==???AB??=889BCHE>>=987/(((()??A?@?:9889;>ADBE??@@??DC222/*****0ABE@A@B44444@BB@@BBAFGKIGEB: NM:i:147 ms:i:7261 AS:i:7228 nn:i:0 tp:A:P cm:i:594 s1:i:3402 s2:i:63 de:f:0.0276 rl:i:0 ru:i:0
= merged_samfile.replace("sam", "bam")
bamfile
= f"samtools view -bS -e 'mapq >= 25' {merged_samfile} > {bamfile}"
exestr #print(exestr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
= bamfile.replace(".bam", "-sort.bam").replace("/bam/", "/sort/")
sortedfile
= f"samtools sort {bamfile} -o {sortedfile}"
exestr1 print(exestr1)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr1}"
= f"samtools index {sortedfile}"
exestr2 print(exestr2)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr2}"
samtools sort /design_build/bam/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged.bam -o /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
samtools index /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
!ls -al sort
total 29746
-rw------- 1 root root 30458496 Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam
-rw------- 1 root root 96 Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam.bai
= sortedfile.replace("-sort", "-consensus").replace("bam", "fasta")
consensusfile
= f"samtools consensus {sortedfile} -o {consensusfile}"
exestr1 print(exestr1)
#!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr1}"
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "samtools --help"
samtools consensus /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam -o /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-consensus.fasta
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
Program: samtools (Tools for alignments in the SAM format)
Version: 1.13 (using htslib 1.13+ds)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
ampliconclip clip oligos from the end of reads
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
import Converts FASTA or FASTQ files to SAM/BAM/CRAM
-- Statistics
bedcov read depth per BED region
coverage alignment depth and percent coverage
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
ampliconstats generate amplicon specific stats
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAM
-- Misc
help [cmd] display this help message or help for [cmd]
version detailed version information
from Bio import SeqIO
= SeqIO.read(consensusfile.replace("/design_build/", ""), "fasta")
cons_seq print(cons_seq)
ID: pACBB_PL
Name: pACBB_PL
Description: pACBB_PL
Number of features: 0
Seq('AATTCATCCTGAACTTATCTAGACCCGACTGGAAAGCGGGCAGTGAGCGCAACG...ATG')
= "/design_build/info/mapping_stats.log"
logfile
= f"samtools flagstat {sortedfile} >> {logfile}"
exestr1 print(exestr1)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr1}"
samtools flagstat /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam >> /design_build/info/mapping_stats.log
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
!cat info/mapping_stats.log
9167 + 0 in total (QC-passed reads + QC-failed reads)
7370 + 0 primary
0 + 0 secondary
1797 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
9167 + 0 mapped (100.00% : N/A)
7370 + 0 primary mapped (100.00% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
!pip install pyfaidx
Collecting pyfaidx
Downloading pyfaidx-0.8.1.1-py3-none-any.whl (28 kB)
Requirement already satisfied: setuptools in /usr/local/lib/python3.10/dist-packages (from pyfaidx) (67.7.2)
Requirement already satisfied: importlib-metadata in /usr/local/lib/python3.10/dist-packages (from pyfaidx) (7.1.0)
Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.10/dist-packages (from importlib-metadata->pyfaidx) (3.19.0)
Installing collected packages: pyfaidx
Successfully installed pyfaidx-0.8.1.1
!faidx --transform bed pACBB_PL.fasta > pACBB_PL.bed
cat pACBB_PL.bed
pACBB_PL 0 7214
= "/design_build/info/mapped_reads.txt"
mapped_readfile = "/design_build/pACBB_PL.bed"
bedfile
= f"bedtools intersect -a {bedfile} -b {sortedfile} -wo > {mapped_readfile}"
exestr1 print(exestr1)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr1}"
bedtools intersect -a /design_build/pACBB_PL.bed -b /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam -wo > /design_build/info/mapped_reads.txt
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
!ls -alh info
total 716K
-rw------- 1 root root 715K Jun 5 02:54 mapped_reads.txt
-rw------- 1 root root 466 Jun 5 02:43 mapping_stats.log
!tail -n 30 info/mapped_reads.txt
pACBB_PL 0 7214 pACBB_PL 6294 7208 0dc5bff4-7df0-499e-9d95-dd2baffa55c3 60 - 914
pACBB_PL 0 7214 pACBB_PL 6301 6523 a2b4db66-56e1-4686-9ad8-72293ff0d6b7 41 + 222
pACBB_PL 0 7214 pACBB_PL 6303 7214 df6cad8b-0549-4ffe-a3b3-ecff002e99e4 60 - 911
pACBB_PL 0 7214 pACBB_PL 6317 7214 26d14fbc-e519-4a72-84f8-d76ef205922c 60 + 897
pACBB_PL 0 7214 pACBB_PL 6382 7214 b1f0d4d9-33f4-4158-8575-e84b372d1018 60 - 832
pACBB_PL 0 7214 pACBB_PL 6395 7208 30b29f15-7289-4db9-b132-33eeccb06226 60 - 813
pACBB_PL 0 7214 pACBB_PL 6396 7214 53f8526e-a6b1-41fb-bd47-51b1df2f98f4 60 - 818
pACBB_PL 0 7214 pACBB_PL 6423 7214 359f8cad-8740-49a4-95d8-306ab7db7161 60 + 791
pACBB_PL 0 7214 pACBB_PL 6498 7214 1619964a-fe7c-4bf8-b178-5ecfc1add0dd 60 - 716
pACBB_PL 0 7214 pACBB_PL 6509 7214 d14e1bc8-7880-4624-936e-9e863d59c956 60 - 705
pACBB_PL 0 7214 pACBB_PL 6536 7214 7e4bf642-5ba7-41fc-8f69-b00053b25fe7 60 + 678
pACBB_PL 0 7214 pACBB_PL 6618 7207 c644b959-dee1-4415-a022-6fb84a1f22d8 60 + 589
pACBB_PL 0 7214 pACBB_PL 6683 7214 69a08152-4449-4dbb-8aa9-f3d30a1d3575 60 - 531
pACBB_PL 0 7214 pACBB_PL 6689 7191 9f7ee30b-459d-4c49-84dc-51824c1732e7 60 - 502
pACBB_PL 0 7214 pACBB_PL 6697 7214 46869993-9b25-419c-bd2c-401a7b50379f 60 - 517
pACBB_PL 0 7214 pACBB_PL 6716 7214 fede98b9-20cc-48d1-a7cd-7261866f7d7e 60 - 498
pACBB_PL 0 7214 pACBB_PL 6722 7214 be5f5927-9b58-4f84-9803-9cb7be7077a3 27 - 492
pACBB_PL 0 7214 pACBB_PL 6769 7214 4488f591-b10b-4dfc-a32d-e22243ded2cf 60 - 445
pACBB_PL 0 7214 pACBB_PL 6984 7214 896713b6-9b3b-4958-8882-bfd6d5b72136 60 - 230
pACBB_PL 0 7214 pACBB_PL 6996 7214 9eb6cdae-e08f-43c0-8ae6-172f1ac5aca9 60 - 218
pACBB_PL 0 7214 pACBB_PL 6998 7214 f15b6fc8-4734-4c1a-abb0-e8842936aa6b 60 + 216
pACBB_PL 0 7214 pACBB_PL 7012 7199 9eb6cdae-e08f-43c0-8ae6-172f1ac5aca9 60 + 187
pACBB_PL 0 7214 pACBB_PL 7040 7208 f4abe4b1-cfcb-4d02-8009-92298f8da641 60 - 168
pACBB_PL 0 7214 pACBB_PL 7053 7214 0e187fe1-6f4f-4fc0-bd15-1bb756b85374 60 - 161
pACBB_PL 0 7214 pACBB_PL 7068 7214 05140fb8-f24b-4478-8159-505cdb96dd45 60 - 146
pACBB_PL 0 7214 pACBB_PL 7071 7214 83cdbaf0-f78e-4f0e-9a85-7bc1ec673eae 60 - 143
pACBB_PL 0 7214 pACBB_PL 7082 7214 196231fa-b3df-4b33-9bd5-9edf232cfe48 60 - 132
pACBB_PL 0 7214 pACBB_PL 7093 7214 454fdd00-183f-44e4-9aa2-f3aa12a01b04 52 + 121
pACBB_PL 0 7214 pACBB_PL 7099 7214 89a4caf9-be0a-49c0-9a93-636cbdd4e8eb 60 - 115
pACBB_PL 0 7214 pACBB_PL 7100 7199 137279f0-bb3a-400f-b39e-492bade3acd6 31 + 99
!cat info/mapped_reads.txt | wc -l
9167
= "/design_build/info/full_mapped_reads.txt"
full_mapped_readfile
= f"bedtools intersect -f 1 -a {bedfile} -b {sortedfile} -wo > {full_mapped_readfile}"
exestr1 print(exestr1)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr1}"
bedtools intersect -f 1 -a /design_build/pACBB_PL.bed -b /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam -wo > /design_build/info/full_mapped_reads.txt
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
!head -n 30 info/full_mapped_reads.txt
pACBB_PL 0 7214 pACBB_PL 0 7214 bb6e8f07-a2c0-4485-b535-6c41c3fed79b 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 0a4649e3-f378-479f-ba8f-17d64ccbda45 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 ce483c40-c300-4f24-888e-84af48a82d63 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 d7da0817-e6f7-4bf1-92ed-8ee8708a51fb 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 611aedb8-f793-47ea-ae2d-0c6c40dbe8c1 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 f1c401d1-432a-43b7-9167-5c08212fa6a9 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 d32cac23-1c9c-4e74-89dd-0d8f7f5aba99 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 6e2227a1-3b3b-4857-bb40-971e206e9bde 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 c020cc11-7bd1-474d-a0a8-549afd6e2c96 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 147a33ab-78b8-4e69-96dc-4a732945b69a 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 b7ef7c70-f67f-46eb-8bea-0c8ebe3c49c8 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 5e1de09f-9e8b-4339-bb5c-8ae9aeb79c14 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 979d5ee6-afab-4142-ac2f-de37ecee859e 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 c746207e-cbdb-4704-ab60-cd1ce22db5ae 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 cb0ef94c-0dc2-4e2e-9c76-f240ee0aea7d 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 f54079d5-0608-4f5e-8685-236cf889f065 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 06d5e1b1-fc9f-4b90-b98d-553c5cd5126d 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 8c3b4f0b-2da5-4324-a5d2-a6a29c6106f8 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 d03eeed8-6f6b-47a2-9507-39edf23d2ee2 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 f569902d-888f-4e2b-9b42-2d37b9e788c0 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 7d396b1b-fccf-471c-a6ca-b866e200f272 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 fada2c2b-9feb-4d9f-9c6c-67eec7e7503d 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 1914effa-f564-4396-a2ac-2bc30e04b6e4 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 66fa0c26-3b75-46c6-9225-24129275fe80 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 985f513e-622f-4424-8526-f92f886992ac 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 8d94fdc7-6955-4dc5-a287-3e455560aca5 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 20bed882-779b-40e7-ad52-a87478df5ccc 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 fc9d4f91-2040-43d1-b3bf-f803c28fc9a8 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 23b5b625-f23f-4b46-97e2-5baece318f9f 60 + 7214
pACBB_PL 0 7214 pACBB_PL 0 7214 233f6d97-8818-4a99-8fb1-c0c841dccfa8 60 + 7214
!cat info/full_mapped_reads.txt | wc -l
1795
Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with “.dict” extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records. (gatk)
https://www.melbournebioinformatics.org.au/tutorials/tutorials/variant_calling_gatk1/variant_calling_gatk1/#2-mark-duplicate-reads
= reference_filename.replace(".fasta", ".dict")
dict_file
= f"gatk CreateSequenceDictionary -R {reference_filename} -O {dict_file}"
exestr print(exestr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
gatk CreateSequenceDictionary -R /design_build/pACBB_PL.fasta -O /design_build/pACBB_PL.dict
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.5.0.0-local.jar CreateSequenceDictionary -R /design_build/pACBB_PL.fasta -O /design_build/pACBB_PL.dict
03:06:50.937 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Jun 05 03:06:51 GMT 2024] CreateSequenceDictionary --OUTPUT /design_build/pACBB_PL.dict --REFERENCE /design_build/pACBB_PL.fasta --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed Jun 05 03:06:51 GMT 2024] Executing as root@adbb3a1816f8 on Linux 6.1.85+ amd64; OpenJDK 64-Bit Server VM 17.0.9+9-Ubuntu-122.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.5.0.0
[Wed Jun 05 03:06:51 GMT 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=113246208
Tool returned:
0
!cat pACBB_PL.dict
@HD VN:1.6
@SQ SN:pACBB_PL LN:7214 M5:592a62e277441af177eea5aef27995a7 UR:file:/design_build/pACBB_PL.fasta
= reference_filename.replace("fasta", "vcf")
vcf_file = sortedfile.replace("-sort", "-sort-withrg")
withrg_file = "pACBB-PL"
rgsm
= f"gatk --java-options '-Xmx10g' AddOrReplaceReadGroups -I {sortedfile} -O {withrg_file} --SORT_ORDER coordinate --RGLB bar --RGPL ont --RGPU 'run barcode' --RGSM {rgsm}"
exestr #print(withrg_file)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10g -jar /gatk/gatk-package-4.5.0.0-local.jar AddOrReplaceReadGroups -I /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam -O /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam --SORT_ORDER coordinate --RGLB bar --RGPL ont --RGPU run barcode --RGSM pACBB-PL
03:22:24.085 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Jun 05 03:22:24 GMT 2024] AddOrReplaceReadGroups --INPUT /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam --OUTPUT /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam --SORT_ORDER coordinate --RGLB bar --RGPL ont --RGPU run barcode --RGSM pACBB-PL --RGID 1 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed Jun 05 03:22:24 GMT 2024] Executing as root@adbb3a1816f8 on Linux 6.1.85+ amd64; OpenJDK 64-Bit Server VM 17.0.9+9-Ubuntu-122.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.5.0.0
INFO 2024-06-05 03:22:24 AddOrReplaceReadGroups Created read-group ID=1 PL=ont LB=bar SM=pACBB-PL
[Wed Jun 05 03:22:27 GMT 2024] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=419430400
Tool returned:
0
!ls -alh sort
total 60M
-rw------- 1 root root 30M Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam
-rw------- 1 root root 96 Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam.bai
-rw------- 1 root root 31M Jun 5 03:22 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam
= f"samtools index {withrg_file}"
exestr !udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
!ls -alh sort
total 60M
-rw------- 1 root root 30M Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam
-rw------- 1 root root 96 Jun 5 03:21 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort.bam.bai
-rw------- 1 root root 31M Jun 5 03:22 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam
-rw------- 1 root root 96 Jun 5 03:23 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam.bai
= reference_filename.replace("fasta", "vcf")
vcf_file
= f"gatk --java-options '-Xmx10g' HaplotypeCaller -I {withrg_file} -R {reference_filename} -O {vcf_file}"
exestr #print(exestr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10g -jar /gatk/gatk-package-4.5.0.0-local.jar HaplotypeCaller -I /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam -R /design_build/pACBB_PL.fasta -O /design_build/pACBB_PL.vcf
03:27:30.109 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
03:27:30.406 INFO HaplotypeCaller - ------------------------------------------------------------
03:27:30.411 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.5.0.0
03:27:30.411 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
03:27:30.412 INFO HaplotypeCaller - Executing as root@adbb3a1816f8 on Linux v6.1.85+ amd64
03:27:30.412 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
03:27:30.412 INFO HaplotypeCaller - Start Date/Time: June 5, 2024 at 3:27:30 AM GMT
03:27:30.413 INFO HaplotypeCaller - ------------------------------------------------------------
03:27:30.413 INFO HaplotypeCaller - ------------------------------------------------------------
03:27:30.415 INFO HaplotypeCaller - HTSJDK Version: 4.1.0
03:27:30.415 INFO HaplotypeCaller - Picard Version: 3.1.1
03:27:30.416 INFO HaplotypeCaller - Built for Spark Version: 3.5.0
03:27:30.417 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:27:30.417 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:27:30.418 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:27:30.419 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:27:30.419 INFO HaplotypeCaller - Deflater: IntelDeflater
03:27:30.420 INFO HaplotypeCaller - Inflater: IntelInflater
03:27:30.420 INFO HaplotypeCaller - GCS max retries/reopens: 20
03:27:30.420 INFO HaplotypeCaller - Requester pays: disabled
03:27:30.421 INFO HaplotypeCaller - Initializing engine
03:27:30.801 INFO HaplotypeCaller - Done initializing engine
03:27:30.853 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
03:27:30.860 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
03:27:30.865 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
03:27:30.876 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
03:27:30.905 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
03:27:30.930 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
03:27:30.931 INFO IntelPairHmm - Available threads: 2
03:27:30.932 INFO IntelPairHmm - Requested threads: 4
03:27:30.932 WARN IntelPairHmm - Using 2 available threads, but 4 were requested
03:27:30.932 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
03:27:30.992 INFO ProgressMeter - Starting traversal
03:27:30.992 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
03:27:39.199 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position pACBB_PL:77 and possibly subsequent; at least 10 samples must have called genotypes
03:28:56.467 INFO ProgressMeter - pACBB_PL:1002 1.4 10 7.0
03:32:13.771 INFO ProgressMeter - pACBB_PL:3014 4.7 20 4.2
03:36:17.536 INFO ProgressMeter - pACBB_PL:4670 8.8 30 3.4
03:42:35.816 INFO ProgressMeter - pACBB_PL:6309 15.1 40 2.7
03:44:46.102 INFO HaplotypeCaller - 0 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
1 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
1 total reads filtered out of 9167 reads processed
03:44:46.102 INFO ProgressMeter - pACBB_PL:6309 17.3 46 2.7
03:44:46.103 INFO ProgressMeter - Traversal complete. Processed 46 total regions in 17.3 minutes.
03:44:46.122 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.168806741
03:44:46.123 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 982.7120195350001
03:44:46.123 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 2.93 sec
03:44:46.125 INFO HaplotypeCaller - Shutting down engine
[June 5, 2024 at 3:44:46 AM GMT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 17.27 minutes.
Runtime.totalMemory()=1501560832
!ls -alh
total 37M
drwx------ 2 root root 4.0K Jun 5 02:26 bam
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
drwx------ 2 root root 4.0K Jun 5 02:56 info
drwx------ 2 root root 4.0K Jun 5 02:14 .ipynb_checkpoints
-rw------- 1 root root 16 Jun 5 02:53 pACBB_PL.bed
-rw------- 1 root root 108 Jun 5 03:06 pACBB_PL.dict
-rw------- 1 root root 7.2K Jun 5 01:56 pACBB_PL.fasta
-rw------- 1 root root 23 Jun 5 02:53 pACBB_PL.fasta.fai
-rw------- 1 root root 15K Jun 5 01:53 pACBB-PL-from_EcoRI_hs.gb
-rw------- 1 root root 22K Jun 5 03:44 pACBB_PL.vcf
-rw------- 1 root root 285 Jun 5 03:44 pACBB_PL.vcf.idx
drwx------ 2 root root 4.0K Jun 5 02:24 sam
drwx------ 2 root root 4.0K Jun 5 03:23 sort
!cat pACBB_PL.vcf
##fileformat=VCFv4.2
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --output /design_build/pACBB_PL.vcf --input /design_build/sort/FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_merged-sort-withrg.bam --reference /design_build/pACBB_PL.fasta --use-posteriors-to-calculate-qual false --dont-use-dragstr-priors false --use-new-qual-calculator true --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --standard-min-confidence-threshold-for-calling 30.0 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotype-assignment-method USE_PLS_TO_ASSIGN --contamination-fraction-to-filter 0.0 --output-mode EMIT_VARIANTS_ONLY --all-site-pls false --flow-likelihood-parallel-threads 0 --flow-likelihood-optimized-comp false --trim-to-haplotype true --exact-matching false --flow-use-t0-tag false --flow-probability-threshold 0.003 --flow-remove-non-single-base-pair-indels false --flow-remove-one-zero-probs false --flow-quantization-bins 121 --flow-fill-empty-bins-value 0.001 --flow-symmetric-indel-probs false --flow-report-insertion-or-deletion false --flow-disallow-probs-larger-than-call false --flow-lump-probs false --flow-retain-max-n-probs-base-format false --flow-probability-scaling-factor 10 --flow-order-cycle-length 4 --keep-boundary-flows false --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --floor-blocks false --indel-size-to-eliminate-in-ref-model 10 --disable-optimizations false --dragen-mode false --dragen-378-concordance-mode false --flow-mode NONE --apply-bqd false --apply-frd false --disable-spanning-event-genotyping false --transform-dragen-mapping-quality false --mapping-quality-threshold-for-genotyping 20 --max-effective-depth-adjustment-for-frd 0 --just-determine-active-regions false --dont-genotype false --do-not-run-physical-phasing false --do-not-correct-overlapping-quality false --use-filtered-reads-for-annotations false --use-flow-aligner-for-stepwise-hc-filtering false --adaptive-pruning false --do-not-recover-dangling-branches false --recover-dangling-heads false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --flow-hmm-engine-min-indel-adjust 6 --flow-hmm-engine-flat-insertion-penatly 45 --flow-hmm-engine-flat-deletion-penatly 45 --pileup-detection false --use-pdhmm false --use-pdhmm-overlap-optimization false --make-determined-haps-from-pd-code false --print-pileupcalling-status false --fallback-gga-if-pdhmm-fails true --pileup-detection-enable-indel-pileup-calling false --pileup-detection-active-region-phred-threshold 0.0 --num-artificial-haplotypes-to-add-per-allele 5 --artifical-haplotype-filtering-kmer-size 10 --pileup-detection-snp-alt-threshold 0.1 --pileup-detection-indel-alt-threshold 0.1 --pileup-detection-absolute-alt-depth 0.0 --pileup-detection-snp-adjacent-to-assembled-indel-range 5 --pileup-detection-snp-basequality-filter 12 --pileup-detection-bad-read-tolerance 0.0 --pileup-detection-proper-pair-read-badness true --pileup-detection-edit-distance-read-badness-threshold 0.08 --pileup-detection-chimeric-read-badness true --pileup-detection-template-mean-badness-threshold 0.0 --pileup-detection-template-std-badness-threshold 0.0 --pileup-detection-filter-assembly-alt-bad-read-tolerance 0.0 --pileup-detection-edit-distance-read-badness-for-assembly-filtering-threshold 0.12 --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --override-fragment-softclip-check false --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --emit-ref-confidence NONE --max-mnp-distance 0 --force-call-filtered-alleles false --reference-model-deletion-quality 30 --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --flow-assembly-collapse-hmer-size 0 --flow-assembly-collapse-partial-mode false --flow-filter-alleles false --flow-filter-alleles-qual-threshold 30.0 --flow-filter-alleles-sor-threshold 3.0 --flow-filter-lone-alleles false --flow-filter-alleles-debug-graphs false --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false --allow-old-rms-mapping-quality-annotation-data false",Version="4.5.0.0",Date="June 5, 2024 at 3:27:30 AM GMT">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##contig=<ID=pACBB_PL,length=7214>
##source=HaplotypeCaller
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT pACBB-PL
pACBB_PL 77 . T G 1325.06 . AC=2;AF=1.00;AN=2;DP=37;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.92;QD=34.72;SOR=3.086 GT:AD:DP:GQ:PL 1/1:0,37:37:99:1339,110,0
pACBB_PL 132 . G GATTTTGTT 90.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.645;DP=7;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=18.12;ReadPosRankSum=1.645;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,3:5:40:98,0,40
pACBB_PL 134 . C T 112.63 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.150;DP=7;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=22.53;ReadPosRankSum=1.150;SOR=1.022 GT:AD:DP:GQ:PL 0/1:2,3:5:40:120,0,40
pACBB_PL 135 . C A 32.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.150;DP=7;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=6.53;ReadPosRankSum=-1.150;SOR=0.446 GT:AD:DP:GQ:PL 0/1:3,2:5:40:40,0,120
pACBB_PL 136 . G A 115.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.91;ReadPosRankSum=1.150;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33
pACBB_PL 138 . G T 115.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.91;ReadPosRankSum=1.150;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33
pACBB_PL 149 . G GGCCCC 51.98 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.99;ReadPosRankSum=0.674;SOR=0.693 GT:AD:DP:GQ:PL 0/1:1,3:4:33:82,0,33
pACBB_PL 153 . AAGC A 70.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.65;ReadPosRankSum=1.383;SOR=0.693 GT:AD:DP:GQ:PL 0/1:2,2:4:43:78,0,43
pACBB_PL 157 . T TTTG 105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=26.40;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,3:4:33:113,0,33
pACBB_PL 160 . A AGGCCTTTTT 83.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.90;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,3:4:33:91,0,33
pACBB_PL 162 . C CGAAAA 115.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.90;ReadPosRankSum=1.150;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33
pACBB_PL 1161 . T TTAA 70.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=5;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=17.65;ReadPosRankSum=-0.431;SOR=0.105 GT:AD:DP:GQ:PL 0/1:2,2:4:78:78,0,78
pACBB_PL 1181 . C T 115.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.91;ReadPosRankSum=-1.150;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33
pACBB_PL 1204 . G A 115.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=28.91;ReadPosRankSum=-1.150;SOR=0.446 GT:AD:DP:GQ:PL 0/1:1,3:4:33:123,0,33
pACBB_PL 1206 . C A 268.01 . AC=2;AF=1.00;AN=2;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.50;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,7:7:21:282,21,0
pACBB_PL 1213 . CT C 92.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.071;DP=13;ExcessHet=0.0000;FS=2.616;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.72;ReadPosRankSum=-0.409;SOR=0.169 GT:AD:DP:GQ:PL 0/1:8,4:12:99:100,0,261
pACBB_PL 1326 . ATTTTGTTAT A 53.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.287;DP=15;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.36;ReadPosRankSum=-0.253;SOR=1.609 GT:AD:DP:GQ:PL 0/1:8,2:10:61:61,0,329
pACBB_PL 1339 . T G 49.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=4.51;ReadPosRankSum=-0.447;SOR=1.371 GT:AD:DP:GQ:PL 0/1:9,2:11:57:57,0,372
pACBB_PL 1347 . GC G 102.36 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.405;DP=11;ExcessHet=0.0000;FS=3.680;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=11.37;ReadPosRankSum=0.272;SOR=0.039 GT:AD:DP:GQ:PL 0/1:4,5:9:94:110,0,94
pACBB_PL 1355 . A AAGC 52.54 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.25;ReadPosRankSum=-0.493;SOR=1.609 GT:AD:DP:GQ:PL 0/1:8,2:10:60:60,0,330
pACBB_PL 1356 . TTTG T 52.54 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.701;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.25;ReadPosRankSum=-0.253;SOR=1.609 GT:AD:DP:GQ:PL 0/1:8,2:10:60:60,0,330
pACBB_PL 1362 . AGGCCTTTTT A 52.54 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.493;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.25;ReadPosRankSum=-0.493;SOR=1.609 GT:AD:DP:GQ:PL 0/1:8,2:10:60:60,0,330
pACBB_PL 1373 . CGAAAA C 49.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=4.51;ReadPosRankSum=-0.447;SOR=1.371 GT:AD:DP:GQ:PL 0/1:9,2:11:57:57,0,372
pACBB_PL 1399 . AT A 93.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=12;ExcessHet=0.0000;FS=3.310;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.80;ReadPosRankSum=-0.816;SOR=2.303 GT:AD:DP:GQ:PL 0/1:6,6:12:99:101,0,149
pACBB_PL 1989 . C G 35.48 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.86;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 2418 . T C 554.06 . AC=2;AF=1.00;AN=2;DP=14;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=26.67;SOR=1.765 GT:AD:DP:GQ:PL 1/1:0,14:14:42:568,42,0
pACBB_PL 3341 . TA T 48.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=3;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.20;ReadPosRankSum=0.000;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,2:3:24:56,0,24
pACBB_PL 3432 . GATT G 115.61 . AC=1;AF=0.500;AN=2;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.90;SOR=2.833 GT:AD:DP:GQ:PL 0/1:1,3:4:32:123,0,32
pACBB_PL 3448 . TA T 166.07 . AC=2;AF=1.00;AN=2;DP=5;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.35;SOR=2.833 GT:AD:DP:GQ:PL 1/1:0,4:4:12:180,12,0
pACBB_PL 4165 . CAAAT C 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.29;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4176 . TTTTCG T 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.42;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4182 . AAAAAG A 35.43 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.13;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4190 . C G 35.48 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.81;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4191 . T TGA 35.43 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=28.71;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4193 . C CGGCG 35.43 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.97;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4194 . CAA C 35.43 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=26.69;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4201 . GGGGGCC G 35.44 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=29.32;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4208 . T TCACGC 35.43 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.77;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4210 . T A 35.47 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=35.30;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4214 . A G 35.48 . AC=2;AF=1.00;AN=2;DP=1;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.58;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4217 . GATAACAA G 35.43 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=36.61;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4226 . A G 35.47 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=32.10;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,1:1:3:45,3,0
pACBB_PL 4714 . GT G 3062.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.671;DP=77;ExcessHet=0.0000;FS=3.813;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=29.96;ReadPosRankSum=0.180;SOR=0.840 GT:AD:DP:GQ:PL 1/1:1,76:77:99:3076,225,0
pACBB_PL 5211 . C CA 1291.03 . AC=2;AF=1.00;AN=2;DP=29;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.82;SOR=2.226 GT:AD:DP:GQ:PL 1/1:0,29:29:87:1305,87,0
pACBB_PL 5243 . TA T 101.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.681;DP=30;ExcessHet=0.0000;FS=8.368;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=3.76;ReadPosRankSum=0.183;SOR=2.833 GT:AD:DP:GQ:PL 0/1:20,7:27:99:109,0,572
pACBB_PL 5326 . G A 1336.06 . AC=2;AF=1.00;AN=2;DP=30;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.83;SOR=2.303 GT:AD:DP:GQ:PL 1/1:0,30:30:90:1350,90,0
pACBB_PL 5403 . C T 1595.06 . AC=2;AF=1.00;AN=2;DP=44;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.94;SOR=1.127 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1915,132,0
pACBB_PL 5897 . AT A 204.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=17;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=12.04;ReadPosRankSum=-0.876;SOR=0.693 GT:AD:DP:GQ:PL 0/1:8,9:17:99:212,0,228
pACBB_PL 6347 . GA G 424.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=46;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.23;ReadPosRankSum=-1.381;SOR=0.576 GT:AD:DP:GQ:PL 0/1:28,18:46:99:432,0,709
pACBB_PL 6553 . GC G 54.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.65;ReadPosRankSum=0.967;SOR=1.179 GT:AD:DP:GQ:PL 0/1:1,3:4:20:62,0,20
pACBB_PL 6635 . T TC 90.61 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.150;DP=4;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=22.65;ReadPosRankSum=1.150;SOR=1.609 GT:AD:DP:GQ:PL 0/1:1,3:4:21:98,0,21
pACBB_PL 6782 . AC A 633.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.318;DP=67;ExcessHet=0.0000;FS=7.513;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.46;ReadPosRankSum=-0.145;SOR=1.780 GT:AD:DP:GQ:PL 0/1:38,29:67:99:641,0,1013
= vcf_file.replace("vcf", "csv")
output_table
= f"gatk VariantsToTable -R {reference_filename} -V {vcf_file} -F CHROM -F POS -F FILTER -F TYPE -GF AD -GF DP --show-filtered -O {output_table}"
exestr #print(exestr)
!udocker --allow-root run -v=/content/drive/MyDrive/design_build:/design_build gatk bash -c "{exestr}"
******************************************************************************
* *
* STARTING 43258f40-d39f-316f-8a89-594ce69950cc *
* *
******************************************************************************
executing: bash
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.5.0.0-local.jar VariantsToTable -R /design_build/pACBB_PL.fasta -V /design_build/pACBB_PL.vcf -F CHROM -F POS -F FILTER -F TYPE -GF AD -GF DP --show-filtered -O /design_build/pACBB_PL.csv
03:45:37.746 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
03:45:38.175 INFO VariantsToTable - ------------------------------------------------------------
03:45:38.180 INFO VariantsToTable - The Genome Analysis Toolkit (GATK) v4.5.0.0
03:45:38.180 INFO VariantsToTable - For support and documentation go to https://software.broadinstitute.org/gatk/
03:45:38.182 INFO VariantsToTable - Executing as root@adbb3a1816f8 on Linux v6.1.85+ amd64
03:45:38.182 INFO VariantsToTable - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
03:45:38.183 INFO VariantsToTable - Start Date/Time: June 5, 2024 at 3:45:37 AM GMT
03:45:38.183 INFO VariantsToTable - ------------------------------------------------------------
03:45:38.183 INFO VariantsToTable - ------------------------------------------------------------
03:45:38.185 INFO VariantsToTable - HTSJDK Version: 4.1.0
03:45:38.185 INFO VariantsToTable - Picard Version: 3.1.1
03:45:38.185 INFO VariantsToTable - Built for Spark Version: 3.5.0
03:45:38.186 INFO VariantsToTable - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:45:38.186 INFO VariantsToTable - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:45:38.186 INFO VariantsToTable - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:45:38.187 INFO VariantsToTable - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:45:38.187 INFO VariantsToTable - Deflater: IntelDeflater
03:45:38.187 INFO VariantsToTable - Inflater: IntelInflater
03:45:38.188 INFO VariantsToTable - GCS max retries/reopens: 20
03:45:38.188 INFO VariantsToTable - Requester pays: disabled
03:45:38.189 INFO VariantsToTable - Initializing engine
03:45:38.727 INFO FeatureManager - Using codec VCFCodec to read file file:///design_build/pACBB_PL.vcf
03:45:38.814 INFO VariantsToTable - Done initializing engine
03:45:38.826 WARN VariantsToTable - Allele-specific fields will only be split if splitting multi-allelic variants is specified (`--split-multi-allelic` or `-SMA`
03:45:38.827 INFO ProgressMeter - Starting traversal
03:45:38.828 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
03:45:38.896 INFO ProgressMeter - unmapped 0.0 52 47272.7
03:45:38.896 INFO ProgressMeter - Traversal complete. Processed 52 total variants in 0.0 minutes.
03:45:38.897 INFO VariantsToTable - Shutting down engine
[June 5, 2024 at 3:45:38 AM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.VariantsToTable done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=312475648
!ls -alh
total 37M
drwx------ 2 root root 4.0K Jun 5 02:26 bam
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_0.fastq.gz
-rw------- 1 root root 19M Jun 5 01:53 FAT01036_pass_barcode01_5eb57f2c_2b75e8f5_1.fastq.gz
drwx------ 2 root root 4.0K Jun 5 02:56 info
drwx------ 2 root root 4.0K Jun 5 02:14 .ipynb_checkpoints
-rw------- 1 root root 16 Jun 5 02:53 pACBB_PL.bed
-rw------- 1 root root 1.7K Jun 5 03:45 pACBB_PL.csv
-rw------- 1 root root 108 Jun 5 03:06 pACBB_PL.dict
-rw------- 1 root root 7.2K Jun 5 01:56 pACBB_PL.fasta
-rw------- 1 root root 23 Jun 5 02:53 pACBB_PL.fasta.fai
-rw------- 1 root root 15K Jun 5 01:53 pACBB-PL-from_EcoRI_hs.gb
-rw------- 1 root root 22K Jun 5 03:44 pACBB_PL.vcf
-rw------- 1 root root 285 Jun 5 03:44 pACBB_PL.vcf.idx
drwx------ 2 root root 4.0K Jun 5 02:24 sam
drwx------ 2 root root 4.0K Jun 5 03:23 sort
import pandas as pd
= pd.read_csv("pACBB_PL.csv", sep='\t')
data
data
CHROM | POS | FILTER | TYPE | pACBB-PL.AD | pACBB-PL.DP | |
---|---|---|---|---|---|---|
0 | pACBB_PL | 77 | PASS | SNP | 0,37 | 37 |
1 | pACBB_PL | 132 | PASS | INDEL | 2,3 | 5 |
2 | pACBB_PL | 134 | PASS | SNP | 2,3 | 5 |
3 | pACBB_PL | 135 | PASS | SNP | 3,2 | 5 |
4 | pACBB_PL | 136 | PASS | SNP | 1,3 | 4 |
5 | pACBB_PL | 138 | PASS | SNP | 1,3 | 4 |
6 | pACBB_PL | 149 | PASS | INDEL | 1,3 | 4 |
7 | pACBB_PL | 153 | PASS | INDEL | 2,2 | 4 |
8 | pACBB_PL | 157 | PASS | INDEL | 1,3 | 4 |
9 | pACBB_PL | 160 | PASS | INDEL | 1,3 | 4 |
10 | pACBB_PL | 162 | PASS | INDEL | 1,3 | 4 |
11 | pACBB_PL | 1161 | PASS | INDEL | 2,2 | 4 |
12 | pACBB_PL | 1181 | PASS | SNP | 1,3 | 4 |
13 | pACBB_PL | 1204 | PASS | SNP | 1,3 | 4 |
14 | pACBB_PL | 1206 | PASS | SNP | 0,7 | 7 |
15 | pACBB_PL | 1213 | PASS | INDEL | 8,4 | 12 |
16 | pACBB_PL | 1326 | PASS | INDEL | 8,2 | 10 |
17 | pACBB_PL | 1339 | PASS | SNP | 9,2 | 11 |
18 | pACBB_PL | 1347 | PASS | INDEL | 4,5 | 9 |
19 | pACBB_PL | 1355 | PASS | INDEL | 8,2 | 10 |
20 | pACBB_PL | 1356 | PASS | INDEL | 8,2 | 10 |
21 | pACBB_PL | 1362 | PASS | INDEL | 8,2 | 10 |
22 | pACBB_PL | 1373 | PASS | INDEL | 9,2 | 11 |
23 | pACBB_PL | 1399 | PASS | INDEL | 6,6 | 12 |
24 | pACBB_PL | 1989 | PASS | SNP | 0,1 | 1 |
25 | pACBB_PL | 2418 | PASS | SNP | 0,14 | 14 |
26 | pACBB_PL | 3341 | PASS | INDEL | 1,2 | 3 |
27 | pACBB_PL | 3432 | PASS | INDEL | 1,3 | 4 |
28 | pACBB_PL | 3448 | PASS | INDEL | 0,4 | 4 |
29 | pACBB_PL | 4165 | PASS | INDEL | 0,1 | 1 |
30 | pACBB_PL | 4176 | PASS | INDEL | 0,1 | 1 |
31 | pACBB_PL | 4182 | PASS | INDEL | 0,1 | 1 |
32 | pACBB_PL | 4190 | PASS | SNP | 0,1 | 1 |
33 | pACBB_PL | 4191 | PASS | INDEL | 0,1 | 1 |
34 | pACBB_PL | 4193 | PASS | INDEL | 0,1 | 1 |
35 | pACBB_PL | 4194 | PASS | INDEL | 0,1 | 1 |
36 | pACBB_PL | 4201 | PASS | INDEL | 0,1 | 1 |
37 | pACBB_PL | 4208 | PASS | INDEL | 0,1 | 1 |
38 | pACBB_PL | 4210 | PASS | SNP | 0,1 | 1 |
39 | pACBB_PL | 4214 | PASS | SNP | 0,1 | 1 |
40 | pACBB_PL | 4217 | PASS | INDEL | 0,1 | 1 |
41 | pACBB_PL | 4226 | PASS | SNP | 0,1 | 1 |
42 | pACBB_PL | 4714 | PASS | INDEL | 1,76 | 77 |
43 | pACBB_PL | 5211 | PASS | INDEL | 0,29 | 29 |
44 | pACBB_PL | 5243 | PASS | INDEL | 20,7 | 27 |
45 | pACBB_PL | 5326 | PASS | SNP | 0,30 | 30 |
46 | pACBB_PL | 5403 | PASS | SNP | 0,44 | 44 |
47 | pACBB_PL | 5897 | PASS | INDEL | 8,9 | 17 |
48 | pACBB_PL | 6347 | PASS | INDEL | 28,18 | 46 |
49 | pACBB_PL | 6553 | PASS | INDEL | 1,3 | 4 |
50 | pACBB_PL | 6635 | PASS | INDEL | 1,3 | 4 |
51 | pACBB_PL | 6782 | PASS | INDEL | 38,29 | 67 |