| File name | EPI-227_S35_L004_dedup.sorted.bam |
| Command generating Sam/Bam file | ID:Bismark VN:v0.19.0 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --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 annotation | No |
| Total chromosomes | 18 |
| Sufficient genome coverage | Yes |
| Total sequences | 9840976 |
| Percent primary alignments | 100.000 |
| Percent sequences failed vendor QC | 0.000 |
| Percent marked duplicate | 0.000 |
| Percent sequences spliced | 0.000 |
| Percent sequences paired | 100.000 |
| Percent sequences properly paired | 100.000 |
| 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 SNPs | 19.272 |
| Percent soft clips | 0.000 |
BamQC Report![[OK]](data:image/png;base64,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)
Basic Statistics
![[FAIL]](data:image/png;base64,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)
Indel Frequencies
