Sequencing data is of an individual (NA12891) from the 1000 genome project.
Google Cloud Platform (GCP), 4 vCPUs, 15 GB RAM
Google Cloud Platform (GCP), 8 vCPUs, 30 GB RAM
Google Cloud Platform (GCP), 24 vCPUs, 32 GB RAM
AWS: c5.18xlarge (72 vCPUs, 144 GB RAM)
AWS: m5.24xlarge (96 vCPUs, 384 GiB RAM)
There are 16 CHRN genes in humans coding for 16 nicotinic acetylcholine receptor subunits.
Nine subunits are classified as alpha (a): chrna1, chrna2, chrna3, chrna4, chrna5, chrna6, chrna7, chrna9, chrna10
Four subunits are classified as beta (b) subumits: chrnb1, chrnb2, chrnb3, chrnb3
One subinit is known as a gamma (chrng) subunit
One subunit is known as delta (chrnd) subunit
Another subunit is classified as an epsilon (chrne) subunit.
chrna1: Chromosome 2, NC_000002.12 (174,747,592..174,764,472, complement)
chrna2: Chromosome 8, NC_000008.11 (27459761..27479296, complement)
chrna3: Chromosome 15, NC_000015.10 (78593052..78621295, complement)
chrna4: Chromosome 20, NC_000020.11 (63,343,310..63,375,471, complement)
chrna5: Chromosome 15, NC_000015.10 (78565520..78595269)
chrna6: Chromosome 8, NC_000008.11 (42752620..42768786, complement)
chrna7: Chromosome 7, NC_000073.6 (63098692..63212526, complement)
chrna9: Chromosome 4, NC_000004.12 (40335329..40355217)
chrna10: Chromosome 11, NC_000011.10 (3665587..3673629, complement)
chrnb1: Chromosome 17, NC_000017.11 (7445087..7457613)
chrnb2: Chromosome 1, NC_000001.11 (154567781..154584708)
chrnb3: Chromosome 8, NC_000008.11 (42697376..42737407)
chrnb4: Chromosome 15, NC_000015.10 (78623282..78655586, complement)
chrng: Chromosome 2, NC_000002.12 (232539727..232546328)
chrnd: Chromosome 2, NC_000002.12 (232526160..232537907)
chrne: Chromosome 17, NC_000017.11 (4897769..4905019, complement)
chrnb2- Chromosome 1, NC_000001.11 (154567781..154584708)
chrna1- Chromosome 2, NC_000002.12 (174747592..174764472, complement)
chrng- Chromosome 2, NC_000002.12 (232539727..232546328)
chrnd- Chromosome 2, NC_000002.12 (232526160..232537907)
chrna9- Chromosome 4, NC_000004.12 (40335329..40355217)
chrna7- Chromosome 7, NC_000073.6 (63098692..63212526, complement)
chrna2- Chromosome 8, NC_000008.11 (27459761..27479296, complement)
chrna6- Chromosome 8, NC_000008.11 (42752620..42768786, complement)
chrnb3- Chromosome 8, NC_000008.11 (42697376..42737407)
chrna10- Chromosome 11, NC_000011.10 (3665587..3673629, complement)
chrna3- Chromosome 15, NC_000015.10 (78593052..78621295, complement)
chrna5- Chromosome 15, NC_000015.10 (78565520..78595269)
chrnb4- Chromosome 15, NC_000015.10 (78623282..78655586, complement)
chrnb1- Chromosome 17, NC_000017.11 (7445087..7457613)
chrne- Chromosome 17, NC_000017.11 (4897769..4905019, complement)
chrna4- Chromosome 20, NC_000020.11 (63343310..63375471, complement)
-rw-rw-r– 1 ubuntu ubuntu 66771360285 May 1 03:50 SRR622458_1.fastq.gz
-rw-rw-r– 1 ubuntu ubuntu 68300205647 May 1 03:42 SRR622458_2.fastq.gz
@SRR622458.1 1/1 TGGGATTGGGGTAGGGCTAGGGCTCGGGTTGGGGATAGGGTGAGGGTTTGGGATAGGGGTAGGGTTAGGGTGTTGGCTAGGGTTAGGGCGAGGGCCAGGGC
@SRR622458.1 1/2 ATAACCCTAACCCTAACCCTAACGCTAACCCTAACCCTAACCCTAACCCTAACAATAACCCTAACCCTAACACTAACCTTACCCCTAACCCTAACCCTCAC
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt .
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb .
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann .
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt .
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac .
$ aws s3 cp s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa .
-rw-rw-r– 1 ubuntu ubuntu 581712 Jan 6 2016 Homo_sapiens_assembly38.dict
-rw-rw-r– 1 ubuntu ubuntu 3249912778 Jan 5 2016 Homo_sapiens_assembly38.fasta
-rw-rw-r– 1 ubuntu ubuntu 487553 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.alt
-rw-rw-r– 1 ubuntu ubuntu 20199 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.amb
-rw-rw-r– 1 ubuntu ubuntu 455474 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.ann
-rw-rw-r– 1 ubuntu ubuntu 3217347004 Nov 6 23:47 Homo_sapiens_assembly38.fasta.64.bwt
-rw-rw-r– 1 ubuntu ubuntu 804336731 Nov 6 23:48 Homo_sapiens_assembly38.fasta.64.pac
-rw-rw-r– 1 ubuntu ubuntu 1608673512 Nov 6 23:48 Homo_sapiens_assembly38.fasta.64.sa
-rw-rw-r– 1 ubuntu ubuntu 160928 Dec 1 2016 Homo_sapiens_assembly38.fasta.fai
…………….
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -M -t 96 -R @RG:SRR622458:P:illumina:FCC1H7WACXX:NA12891 Homo_sapiens_assembly38.fasta SRR622458_1.fastq.gz SRR622458_2.fastq.gz
[main] Real time: 27098.059 sec; CPU: 1337083.667 sec
[bam_sort_core] merging from 947 files and 1 in-memory blocks…
2448099046 + 0 in total (QC-passed reads + QC-failed reads)
11520983 + 0 secondary
12880297 + 0 supplementary
0 + 0 duplicates
2368472627 + 0 mapped (96.75% : N/A)
2423697766 + 0 paired in sequencing
1211848883 + 0 read1
1211848883 + 0 read2
2258885338 + 0 properly paired (93.20% : N/A)
2317266676 + 0 with itself and mate mapped
26804671 + 0 singletons (1.11% : N/A)
31022454 + 0 with mate mapped to a different chr
17456435 + 0 with mate mapped to a different chr (mapQ>=5)
2,448,099,046 + 0 in total (QC-passed reads + QC-failed reads)
11520983 + 0 secondary
12880297 + 0 supplementary
0 + 0 duplicates
2368472627 + 0 mapped (96.75%:N/A)
2423697766 + 0 paired in sequencing
1211848883 + 0 read1
1211848883 + 0 read2
2258885338 + 0 properly paired (93.20%:N/A)
2317266676 + 0 with itself and mate mapped
26804671 + 0 singletons (1.11%:N/A)
31022454 + 0 with mate mapped to a different chr
17456435 + 0 with mate mapped to a different chr (mapQ>=5)
-rw-rw-r– 1 b0d2647 b0d2647 189005777011 May 1 17:46 SRR622458.bam
-rw-rw-r– 1 b0d2647 b0d2647 9777672 May 1 19:12 SRR622458.bam.bai
……………
[Fri May 03 21:01:34 UTC 2019] picard.sam.ValidateSamFile done. Elapsed time: 443.41 minutes.
Runtime.totalMemory()=1916272640
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Tool returned: 3
## HISTOGRAM java.lang.String
Error Type Count
ERROR:INVALID_TAG_NM 207087
………………………
INFO 2019-05-04 23:41:16 MarkDuplicates Will retain up to 112,852,992 duplicate indices before spilling to disk.
INFO 2019-05-04 23:41:16 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2019-05-04 23:41:16 SortingCollection Creating merging iterator from 92 files
……………………………….
INFO 2019-05-04 23:53:09 SortingCollection Creating merging iterator from 185 files
…………………………………..
INFO 2019-05-05 00:09:35 MarkDuplicates Marking 126,416,116 records as duplicates.
INFO 2019-05-05 00:09:35 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2019-05-05 00:09:35 MarkDuplicates Reads are assumed to be ordered by: coordinate
………………….
[Sun May 05 04:59:44 UTC 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 684.96 minutes.
Runtime.totalMemory()=2610429952
Tool returned: 0
……………….
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
P 26804671 1158633338 24401280 79626419 12149656 57133230 0 0.05393 11358780886
-rw-rw-r– 1 b0d2647 b0d2647 256414514748 May 4 05:07 SRR622458.fxNmMdUqTag.bam
-rw-rw-r– 1 b0d2647 b0d2647 9791560 May 4 17:18 SRR622458.fxNmMdUqTag.bam.bai
-rw-rw-r– 1 b0d2647 b0d2647 4604 May 5 04:59 SRR622458.fxNmMdUqTag.dupMetrics.txt
-rw-rw-r– 1 b0d2647 b0d2647 259148164965 May 5 04:59 SRR622458.fxNmMdUqTag.mdup.bam
#!/bin/bash
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr2:174,747,592-174,764,472 -O SRR622458.fxNmMdUqTag.mdup.chrna1.vcf >& hcall.58.chrna1.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr8:27,459,761-27,479,296 -O SRR622458.fxNmMdUqTag.mdup.chrna2.vcf >& hcall.58.chrna2.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr15:78593052-78621295 -O SRR622458.fxNmMdUqTag.mdup.chrna3.vcf >& hcall.58.chrna3.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr20:63343310-63375471 -O SRR622458.fxNmMdUqTag.mdup.chrna4.vcf >& hcall.58.chrna4.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr15:78565520-78595269 -O SRR622458.fxNmMdUqTag.mdup.chrna5.vcf >& hcall.58.chrna5.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr8:42752620-42768786 -O SRR622458.fxNmMdUqTag.mdup.chrna6.vcf >& hcall.58.chrna6.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr7:63098692-63212526 -O SRR622458.fxNmMdUqTag.mdup.chrna7.vcf >& hcall.58.chrna7.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr4:40335329-40355217 -O SRR622458.fxNmMdUqTag.mdup.chrna9.vcf >& hcall.58.chrna9.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr11:3665587-3673629 -O SRR622458.fxNmMdUqTag.mdup.chrna10.vcf >& hcall.58.chrna10.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr17:7445087-7457613 -O SRR622458.fxNmMdUqTag.mdup.chrnb1.vcf >& hcall.58.chrnb1.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr1:154567781-154584708 -O SRR622458.fxNmMdUqTag.mdup.chrnb2.vcf >& hcall.58.chrnb2.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr8:42697376-42737407 -O SRR622458.fxNmMdUqTag.mdup.chrnb3.vcf >& hcall.58.chrnb3.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr15:78623282-78655586 -O SRR622458.fxNmMdUqTag.mdup.chrnb4.vcf >& hcall.58.chrnb4.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr2:232539727-232546328 -O SRR622458.fxNmMdUqTag.mdup.chrng.vcf >& hcall.58.chrng.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr2:232526160-232537907 -O SRR622458.fxNmMdUqTag.mdup.chrnd.vcf >& hcall.58.chrnd.log &
nohup gatk HaplotypeCaller -R Homo_sapiens_assembly38.fasta -I SRR622458.fxNmMdUqTag.mdup.bam -L chr17:4897769-4905019 -O SRR622458.fxNmMdUqTag.mdup.chrne.vcf >& hcall.58.chrne.log &
-rw-rw-r-- 1 b0d2647 b0d2647 181598 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna1.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 115469 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna1.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 178462 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna10.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114090 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna10.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 185104 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna2.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114317 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna2.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 194287 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna3.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114717 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna3.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 193980 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna4.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114597 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna4.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 188353 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna5.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114715 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna5.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 176862 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna6.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114421 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrna6.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 203559 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna7.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 122003 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna7.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 186797 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna9.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114419 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrna9.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 179752 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnb1.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114167 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnb1.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 179940 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnb2.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 115307 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnb2.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 184094 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrnb3.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114435 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrnb3.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 188849 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrnb4.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114716 May 5 19:52 SRR622458.fxNmMdUqTag.mdup.chrnb4.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 176133 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnd.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 115893 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrnd.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 179197 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrne.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 114096 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrne.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 178127 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrng.vcf
-rw-rw-r-- 1 b0d2647 b0d2647 115892 May 5 19:51 SRR622458.fxNmMdUqTag.mdup.chrng.vcf.idx
-rw-rw-r-- 1 b0d2647 b0d2647 6363 May 5 19:51 hcall.58.chrna1.log
-rw-rw-r-- 1 b0d2647 b0d2647 6163 May 5 19:51 hcall.58.chrna10.log
-rw-rw-r-- 1 b0d2647 b0d2647 6347 May 5 19:51 hcall.58.chrna2.log
-rw-rw-r-- 1 b0d2647 b0d2647 6472 May 5 19:52 hcall.58.chrna3.log
-rw-rw-r-- 1 b0d2647 b0d2647 6469 May 5 19:51 hcall.58.chrna4.log
-rw-rw-r-- 1 b0d2647 b0d2647 6470 May 5 19:52 hcall.58.chrna5.log
-rw-rw-r-- 1 b0d2647 b0d2647 6237 May 5 19:51 hcall.58.chrna6.log
-rw-rw-r-- 1 b0d2647 b0d2647 6594 May 5 19:52 hcall.58.chrna7.log
-rw-rw-r-- 1 b0d2647 b0d2647 6455 May 5 19:52 hcall.58.chrna9.log
-rw-rw-r-- 1 b0d2647 b0d2647 6348 May 5 19:51 hcall.58.chrnb1.log
-rw-rw-r-- 1 b0d2647 b0d2647 6351 May 5 19:51 hcall.58.chrnb2.log
-rw-rw-r-- 1 b0d2647 b0d2647 6476 May 5 19:52 hcall.58.chrnb3.log
-rw-rw-r-- 1 b0d2647 b0d2647 6462 May 5 19:52 hcall.58.chrnb4.log
-rw-rw-r-- 1 b0d2647 b0d2647 6240 May 5 19:51 hcall.58.chrnd.log
-rw-rw-r-- 1 b0d2647 b0d2647 6149 May 5 19:51 hcall.58.chrne.log
-rw-rw-r-- 1 b0d2647 b0d2647 6229 May 5 19:51 hcall.58.chrng.log
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna1.vcf
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 37
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 28
SN 0 number of MNPs: 0
SN 0 number of indels: 9
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna2.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna2.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 47
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 43
SN 0 number of MNPs: 0
SN 0 number of indels: 4
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna3.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna3.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 85
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 68
SN 0 number of MNPs: 0
SN 0 number of indels: 17
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna4.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna4.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 98
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 80
SN 0 number of MNPs: 0
SN 0 number of indels: 18
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 1
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna5.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna5.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 60
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 42
SN 0 number of MNPs: 0
SN 0 number of indels: 18
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 1
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna6.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna6.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 8
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 4
SN 0 number of MNPs: 0
SN 0 number of indels: 4
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna7.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna7.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 155
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 119
SN 0 number of MNPs: 0
SN 0 number of indels: 36
SN 0 number of others: 0
SN 0 number of multiallelic sites: 5
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna9.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna9.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 56
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 47
SN 0 number of MNPs: 0
SN 0 number of indels: 9
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrna10.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrna10.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 15
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 15
SN 0 number of MNPs: 0
SN 0 number of indels: 0
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrnb1.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrnb1.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 21
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 15
SN 0 number of MNPs: 0
SN 0 number of indels: 6
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrnb2.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrnb2.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 22
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 17
SN 0 number of MNPs: 0
SN 0 number of indels: 5
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrnb3.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrnb3.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 46
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 35
SN 0 number of MNPs: 0
SN 0 number of indels: 11
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrnb4.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrnb4.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 66
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 48
SN 0 number of MNPs: 0
SN 0 number of indels: 18
SN 0 number of others: 3
SN 0 number of multiallelic sites: 3
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrng.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrng.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 15
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 11
SN 0 number of MNPs: 0
SN 0 number of indels: 4
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrnd.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrnd.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 5
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 4
SN 0 number of MNPs: 0
SN 0 number of indels: 1
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
# This file was produced by bcftools stats (1.9+htslib-1.9) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats SRR622458.fxNmMdUqTag.mdup.chrne.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 SRR622458.fxNmMdUqTag.mdup.chrne.vcf
# SN, Summary numbers:
# number of records .. number of data rows in the VCF
# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
# number of SNPs .. number of rows with a SNP
# number of MNPs .. number of rows with a MNP, such as CC>TT
# number of indels .. number of rows with an indel
# number of others .. number of rows with other type, for example a symbolic allele or
# a complex substitution, such as ACT>TCGA
# number of multiallelic sites .. number of rows with multiple alternate alleles
# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
# Note that rows containing multiple types will be counted multiple times, in each
# counter. For example, a row with a SNP and an indel increments both the SNP and
# the indel counter.
#
# SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 19
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 18
SN 0 number of MNPs: 0
SN 0 number of indels: 1
SN 0 number of others: 0
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0