BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524702.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 = 717,477 number of mapped reads = 660,782 (92.1%) number of supplementary alignments = 2,543 (0.35%) number of secondary alignments = 0 number of mapped bases = 39,355,200 bp number of sequenced bases = 39,343,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,209 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1063 >>>>>>> ACTG content number of A's = 10,745,395 bp (27.31%) number of C's = 7,040,357 bp (17.89%) number of T's = 12,272,993 bp (31.19%) number of G's = 9,279,212 bp (23.59%) number of N's = 5,395 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 198,034 number of insertions = 3,402 mapped reads with insertion percentage = 0.51% number of deletions = 7,509 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.02% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1498X There is a 1.2% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 3158605 0.012672405738961027 0.23462268694212512 chr2 243199373 3330269 0.013693575599802225 0.1917734194160748 chr3 198022430 2621993 0.013240888923542651 0.1198620165448766 chr4 191154276 2563962 0.013413050723489963 0.12826319802488234 chr5 180915260 2408823 0.013314647973863565 0.12054844848933882 chr6 171115067 2277126 0.013307571565278935 0.12856388239602415 chr7 159138663 2183438 0.013720349026684986 0.16858487419652576 chr8 146364022 2038335 0.013926475729124197 0.16405602949284512 chr9 141213431 1653804 0.011711378926838765 0.1316602818434189 chr10 135534747 1882447 0.01388903614510012 0.15762070224074604 chr11 135006516 1759313 0.013031319169809551 0.13588068666001232 chr12 133851895 1750748 0.013079740111262526 0.11982396410474228 chr13 115169878 1233155 0.01070727017701625 0.10755976319936812 chr14 107349540 1173121 0.010928048690287821 0.1102665893037404 chr15 102531392 1124654 0.01096887478129625 0.10907962166012924 chr16 90354753 1139518 0.01261159996751914 0.12249221049377146 chr17 81195210 1062463 0.013085291607719225 0.12063914806447602 chr18 78077248 1044570 0.013378673387668582 0.20570700621427068 chr19 59128983 786245 0.013297116914728603 0.1735158377931072 chr20 63025520 822441 0.013049333032079703 0.12021651868721493 chr21 48129895 526660 0.010942471409921006 0.11528750071747808 chr22 51304566 440858 0.008592958373334646 0.0965410895393064 chrMT 16571 18140 1.0946834831935308 1.1433503892237629 chrX 155270560 2217102 0.014278959256667844 0.12922865540710501 chrY 59373566 137410 0.002314329578924062 0.09356346811992333