BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524348.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 = 3,197,549 number of mapped reads = 2,932,650 (91.72%) number of supplementary alignments = 13,284 (0.42%) number of secondary alignments = 0 number of mapped bases = 171,432,437 bp number of sequenced bases = 171,384,121 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,970 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4466 >>>>>>> ACTG content number of A's = 40,466,751 bp (23.61%) number of C's = 33,915,176 bp (19.79%) number of T's = 56,231,375 bp (32.81%) number of G's = 40,747,550 bp (23.78%) number of N's = 23,269 bp (0.01%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 878,132 number of insertions = 12,908 mapped reads with insertion percentage = 0.44% number of deletions = 31,176 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0554X std coverageData = 0.4802X There is a 4.68% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14363147 0.05762532082116658 0.9576792057037696 chr2 243199373 11143620 0.04582092405312246 0.6615958163097191 chr3 198022430 12070369 0.060954554491630064 0.2877864993919186 chr4 191154276 8871370 0.046409477128306564 0.30918340067746275 chr5 180915260 9982248 0.05517637373431075 0.27153588928150246 chr6 171115067 11070791 0.06469793218150685 0.33208861087064045 chr7 159138663 7863302 0.04941163794998077 0.5704279232407805 chr8 146364022 17684890 0.12082812263795265 0.5953811775414314 chr9 141213431 7152831 0.05065262524497404 0.3624120176763136 chr10 135534747 8829852 0.06514825308966711 0.4628686094326523 chr11 135006516 8259633 0.06117951373547037 0.3932297082868879 chr12 133851895 6727448 0.05026038667588531 0.2655248452398682 chr13 115169878 4280690 0.0371684860168038 0.22442871071078177 chr14 107349540 3595819 0.03349636151212199 0.23296752510992288 chr15 102531392 5304646 0.05173679881377208 0.2621575717097249 chr16 90354753 5377376 0.059514035747516236 0.31014388220199374 chr17 81195210 5324149 0.06557220555251966 0.3367275281461901 chr18 78077248 4008173 0.05133599227267846 0.7201072592243073 chr19 59128983 3053549 0.05164217013507572 0.6108445534956772 chr20 63025520 3953794 0.06273322298649817 0.29508433048368304 chr21 48129895 2472848 0.05137862860494501 0.2981697839834371 chr22 51304566 1275887 0.02486887814234702 0.18282083366744373 chrMT 16571 13632 0.822641964878402 1.0828272806527752 chrX 155270560 8250564 0.05313669249341279 0.3111899152178421 chrY 59373566 501809 0.008451724122482386 0.24697108706201693