BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236104.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,803,012 number of mapped reads = 2,435,526 (86.89%) number of supplementary alignments = 16,049 (0.57%) number of secondary alignments = 0 number of mapped bases = 160,347,753 bp number of sequenced bases = 160,263,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,747 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8905 >>>>>>> ACTG content number of A's = 45,540,484 bp (28.42%) number of C's = 29,247,314 bp (18.25%) number of T's = 49,834,507 bp (31.1%) number of G's = 35,639,314 bp (22.24%) number of N's = 1,563 bp (0%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,295,400 number of insertions = 13,043 mapped reads with insertion percentage = 0.53% number of deletions = 48,638 mapped reads with deletion percentage = 1.97% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.573X There is a 4.41% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13342917 0.05353213142044689 0.9669566363282907 chr2 243199373 8868033 0.03646404548913044 0.5772723162718707 chr3 198022430 11668963 0.05892748109393466 0.2713890668711233 chr4 191154276 5983763 0.03130331753604089 0.273012696392623 chr5 180915260 8937000 0.04939881798804589 0.2557234255245753 chr6 171115067 18648871 0.10898438884987258 0.5895279320122334 chr7 159138663 9222143 0.057950361189097084 0.7311963036995947 chr8 146364022 12510089 0.08547243256269632 1.3127563837526213 chr9 141213431 6233996 0.04414591413758653 0.5233193074071619 chr10 135534747 6489792 0.047882865048621076 0.5020535127723829 chr11 135006516 5444540 0.04032797942878549 0.3628703305558189 chr12 133851895 6360493 0.0475188864528216 0.26293009337249956 chr13 115169878 6166772 0.053545007662507034 0.25884917223127796 chr14 107349540 5037285 0.046924141454169246 0.2865364239862879 chr15 102531392 4603464 0.04489809325908693 0.2549667769664525 chr16 90354753 3208679 0.03551201119436406 0.29374529676673555 chr17 81195210 4132854 0.05090021936023073 0.32899201625095026 chr18 78077248 3873630 0.049612788606483674 0.9363932467192374 chr19 59128983 2985035 0.050483449038857986 0.6511031140449764 chr20 63025520 3396658 0.05389337525497608 0.2761093871105552 chr21 48129895 2501479 0.05197349796836249 0.3191748115860186 chr22 51304566 1072302 0.02090071281374839 0.15942910200184082 chrMT 16571 53538 3.230824935127633 2.77222553335259 chrX 155270560 9129590 0.058797945985381905 0.3235194624503174 chrY 59373566 475867 0.008014795675233655 0.23005810129905024