BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716462.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 = 1,204,356 number of mapped reads = 1,027,218 (85.29%) number of supplementary alignments = 3,914 (0.32%) number of secondary alignments = 0 number of mapped bases = 57,903,642 bp number of sequenced bases = 57,885,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,692 duplication rate = 1.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2151 >>>>>>> ACTG content number of A's = 14,165,316 bp (24.47%) number of C's = 11,127,753 bp (19.22%) number of T's = 18,309,179 bp (31.63%) number of G's = 14,282,876 bp (24.67%) number of N's = 870 bp (0%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 302,542 number of insertions = 4,640 mapped reads with insertion percentage = 0.45% number of deletions = 11,117 mapped reads with deletion percentage = 1.07% homopolymer indels = 39.07% >>>>>>> Coverage mean coverageData = 0.0187X std coverageData = 0.1874X There is a 1.73% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 4876979 0.01956656709794115 0.21271806241833613 chr2 243199373 5576469 0.022929619148319105 0.2639512755104345 chr3 198022430 4086614 0.020637126814371482 0.16602609145006855 chr4 191154276 2739590 0.01433182692706283 0.133740687806626 chr5 180915260 2988640 0.016519557277810615 0.1356254789795542 chr6 171115067 3253420 0.019013053946909303 0.15656391128439337 chr7 159138663 2876649 0.018076367777452047 0.3281265349090399 chr8 146364022 4752134 0.0324679107274054 0.20921437381215008 chr9 141213431 2411547 0.017077320357721498 0.15295093621812064 chr10 135534747 2820419 0.020809564059613435 0.23607585963816716 chr11 135006516 1964995 0.014554816006065958 0.14582103831100754 chr12 133851895 2752874 0.02056656724957088 0.15782394066305772 chr13 115169878 1516150 0.013164466493573954 0.12127957315401058 chr14 107349540 1881536 0.017527192012187477 0.14412007026203089 chr15 102531392 1388548 0.01354266213414912 0.12654953997825957 chr16 90354753 1808302 0.02001335779203558 0.15562211235272438 chr17 81195210 2563098 0.0315671084538115 0.19451383853200535 chr18 78077248 1332844 0.017070837332791237 0.20382559762460936 chr19 59128983 1275641 0.021573870127277513 0.21557509164831076 chr20 63025520 1297917 0.020593515134821577 0.15419401312091957 chr21 48129895 606818 0.012607922788944376 0.12363983027380228 chr22 51304566 887177 0.017292359514355895 0.13974434338808606 chrMT 16571 44144 2.6639309637318207 2.2974116343757838 chrX 155270560 2062005 0.01328007704744544 0.13679473652169036 chrY 59373566 139132 0.0023433323846507722 0.07053007188809111