BamQCBamQC Report
Mon 12 Aug 2019


[OK]Basic Statistics

File nameEPI-227_S35_L004_dedup.sorted.bam
Command generating Sam/Bam fileID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2- --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
Has annotationNo
Total chromosomes18
Sufficient genome coverageYes
Total sequences9840976
Percent primary alignments100.000
Percent sequences failed vendor QC 0.000
Percent marked duplicate 0.000
Percent sequences spliced 0.000
Percent sequences paired100.000
Percent sequences properly paired100.000
Percent singletons 0.000
Percent sequences unmapped 0.000
Percent sequences without MD Tag String 0.000
Percent sequences without Cigar String 0.000
Percent sequences with inconsistent Cigar or MD Tag Strings 0.000
Percent sequences discarded for variant call detection 0.000
Percent indels 1.638 (Ins: 1.121; Del: 0.517)
Percent SNPs19.272
Percent soft clips 0.000

[OK]Genome Coverage

Genome Coverage

[OK]Chromosome Read Density

Chromsome Density Graph

[FAIL]Indel Frequencies

Indel Frequencies

[FAIL]SNP Frequencies

SNP Frequencies

[FAIL]SNP Frequencies by Type

SNP Frequencies by Type

[FAIL]Mapping Quality Distribution

Mapping Quality Value Distribution

[FAIL]Insert Length Distribution

Paired Read Insert Length Distribution ( 10000 bp max size and 0.000 % unpaired reads )