BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524583.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 = 996,569 number of mapped reads = 907,302 (91.04%) number of supplementary alignments = 3,906 (0.39%) number of secondary alignments = 0 number of mapped bases = 52,915,700 bp number of sequenced bases = 52,896,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,466 duplication rate = 2.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0876 >>>>>>> ACTG content number of A's = 13,234,000 bp (25.02%) number of C's = 9,491,526 bp (17.94%) number of T's = 17,343,041 bp (32.79%) number of G's = 12,827,120 bp (24.25%) number of N's = 781 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 278,009 number of insertions = 3,306 mapped reads with insertion percentage = 0.36% number of deletions = 11,583 mapped reads with deletion percentage = 1.27% homopolymer indels = 43.97% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.181X There is a 1.58% of reference with a coverageData >= 1X There is a 0.09% 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 5213688 0.020917452398242973 0.3161079541635365 chr2 243199373 4140371 0.01702459570074632 0.1989511233054279 chr3 198022430 2891257 0.014600654077419412 0.12861886236157374 chr4 191154276 3017808 0.015787290052564663 0.14369399386001014 chr5 180915260 2900158 0.01603047747326566 0.13454946348918698 chr6 171115067 2322054 0.013570131728961075 0.14508987166844897 chr7 159138663 2646894 0.016632626855737753 0.2136951628294895 chr8 146364022 4916515 0.03359100776828885 0.2158265690284205 chr9 141213431 2246430 0.015908047726706676 0.156391149854074 chr10 135534747 2789032 0.020577985068286585 0.18832055013006235 chr11 135006516 1844615 0.013663155339850411 0.1602296089339599 chr12 133851895 2489938 0.01860218714124294 0.14437877539592328 chr13 115169878 1082635 0.009400331222023176 0.10284085719197748 chr14 107349540 1248992 0.01163481464382614 0.11575215221950642 chr15 102531392 1394482 0.013600537092093707 0.1266067363392751 chr16 90354753 1632837 0.01807140129086513 0.14890458807424145 chr17 81195210 1802612 0.022200964810608903 0.1647177741284094 chr18 78077248 1291531 0.016541707515100944 0.25686243403019104 chr19 59128983 1030982 0.01743615309602061 0.21469712270190625 chr20 63025520 1476161 0.02342163936132538 0.16295767570414904 chr21 48129895 725259 0.015068784172498195 0.13615391279157896 chr22 51304566 413917 0.008067839419984568 0.0948338736391985 chrMT 16571 12737 0.7686319473779494 0.9355133925693877 chrX 155270560 3208582 0.02066445822054097 0.16211106544879358 chrY 59373566 176213 0.0029678695734731515 0.10154143685525524