BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524960.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 = 1,347,769 number of mapped reads = 1,249,398 (92.7%) number of supplementary alignments = 3,469 (0.26%) number of secondary alignments = 0 number of mapped bases = 73,286,966 bp number of sequenced bases = 73,262,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,106 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1668 >>>>>>> ACTG content number of A's = 18,415,330 bp (25.14%) number of C's = 13,666,330 bp (18.65%) number of T's = 23,212,378 bp (31.68%) number of G's = 17,967,384 bp (24.52%) number of N's = 831 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 358,676 number of insertions = 4,648 mapped reads with insertion percentage = 0.37% number of deletions = 14,202 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.233X There is a 2.18% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 7688659 0.030847100677835422 0.43296069860604214 chr2 243199373 6729153 0.027669285973035793 0.27109504176961724 chr3 198022430 4098065 0.02069495359692334 0.1536951617652018 chr4 191154276 4703650 0.024606564385721615 0.1754181489320089 chr5 180915260 3146956 0.01739464100485498 0.14296861088756693 chr6 171115067 4959012 0.0289805689641579 0.241752013851305 chr7 159138663 4642460 0.02917242053240073 0.3093681887744968 chr8 146364022 4308945 0.029439919326622495 0.23160072194525558 chr9 141213431 1991786 0.014104791491115317 0.18367500926237842 chr10 135534747 3620815 0.02671503123844692 0.22072424161353726 chr11 135006516 3069744 0.02273774696919073 0.2066275318825974 chr12 133851895 3954711 0.02954542406739927 0.18423831637207536 chr13 115169878 2009751 0.017450318042361735 0.1416034100966688 chr14 107349540 1707567 0.015906607517833796 0.13952849073103707 chr15 102531392 2035496 0.019852417491805826 0.15962108129372024 chr16 90354753 2337558 0.02587089137413723 0.178513263536042 chr17 81195210 1841656 0.022681830615377433 0.20950438134579186 chr18 78077248 1480398 0.018960683655243588 0.2958266996912736 chr19 59128983 1835221 0.0310375877765393 0.2753749506346266 chr20 63025520 1795301 0.028485302461606028 0.1830051511766608 chr21 48129895 1042218 0.021654275372925705 0.1618603930438958 chr22 51304566 956295 0.01863956903952759 0.14428897944729482 chrMT 16571 19059 1.1501418140124313 1.3095151598740042 chrX 155270560 3118148 0.020082029716386673 0.17279942109446333 chrY 59373566 194342 0.0032732074741813554 0.08120806099912284