BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716806.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 601,647 number of mapped reads = 530,391 (88.16%) number of supplementary alignments = 2,597 (0.43%) number of secondary alignments = 0 number of mapped bases = 30,587,966 bp number of sequenced bases = 30,578,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,342 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6531 >>>>>>> ACTG content number of A's = 7,289,940 bp (23.84%) number of C's = 6,354,148 bp (20.78%) number of T's = 9,660,421 bp (31.59%) number of G's = 7,274,022 bp (23.79%) number of N's = 416 bp (0%) GC percentage = 44.57% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 154,854 number of insertions = 2,238 mapped reads with insertion percentage = 0.42% number of deletions = 5,812 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.32% >>>>>>> Coverage mean coverageData = 0.0099X std coverageData = 0.1215X There is a 0.93% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 2515135 0.010090787296373476 0.188707189365736 chr2 243199373 2591089 0.010654176316482527 0.13797335460732416 chr3 198022430 2018999 0.010195809636312411 0.10540393719098395 chr4 191154276 1850871 0.009682603176504406 0.1053682706836358 chr5 180915260 1822661 0.010074667001556419 0.10445063214420029 chr6 171115067 1759431 0.010282151249720166 0.11304389924393131 chr7 159138663 1674303 0.010521032214528533 0.13723174271058164 chr8 146364022 1489994 0.010180056407578086 0.11417997371883076 chr9 141213431 1268922 0.008985844979575632 0.10618784436189228 chr10 135534747 1490008 0.01099354986806446 0.12290825363459251 chr11 135006516 1409333 0.010438999847977708 0.11835583208419037 chr12 133851895 1351691 0.010098407646750164 0.10510861495914166 chr13 115169878 949294 0.008242554533226127 0.09398082808750025 chr14 107349540 924675 0.008613683859288079 0.09806547168710707 chr15 102531392 912085 0.008895665826910846 0.09910114797161425 chr16 90354753 916886 0.010147623335321387 0.107066143138285 chr17 81195210 872647 0.010747518234142137 0.10968727840386965 chr18 78077248 793275 0.010160130131635787 0.14254053457816324 chr19 59128983 673186 0.011385042763208019 0.14476375291323024 chr20 63025520 663707 0.010530765950046901 0.10747534965898063 chr21 48129895 400173 0.008314437419819843 0.09847335970484258 chr22 51304566 394383 0.007687093581495261 0.09150086294769524 chrMT 16571 26365 1.5910325267032768 1.5367050098648891 chrX 155270560 1719732 0.011075711970124923 0.11344393788064809 chrY 59373566 99121 0.001669446635561691 0.05454053346816514