BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525141.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 = 987,493 number of mapped reads = 878,614 (88.97%) number of supplementary alignments = 25,072 (2.54%) number of secondary alignments = 0 number of mapped bases = 67,842,268 bp number of sequenced bases = 67,812,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,114 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1463 >>>>>>> ACTG content number of A's = 17,460,040 bp (25.75%) number of C's = 13,531,031 bp (19.95%) number of T's = 20,562,299 bp (30.32%) number of G's = 16,256,046 bp (23.97%) number of N's = 2,634 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 527,150 number of insertions = 5,607 mapped reads with insertion percentage = 0.63% number of deletions = 17,301 mapped reads with deletion percentage = 1.94% homopolymer indels = 42.55% >>>>>>> Coverage mean coverageData = 0.0219X std coverageData = 0.2826X There is a 2.01% of reference with a coverageData >= 1X There is a 0.11% 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 6728473 0.026994809373012556 0.626055256265691 chr2 243199373 5826762 0.023958787097695354 0.3076340088641206 chr3 198022430 4423827 0.022340029864293655 0.1588850937456635 chr4 191154276 4241402 0.022188371030737498 0.1692022175906117 chr5 180915260 4072407 0.02251002485915229 0.16027774568241251 chr6 171115067 3853769 0.02252150595248284 0.17915521476144686 chr7 159138663 3756577 0.023605684056802714 0.348884029107939 chr8 146364022 1911236 0.013058099756236542 0.26767008645873164 chr9 141213431 2800987 0.019835131688004947 0.22497059689646906 chr10 135534747 3108497 0.022935055908578188 0.2719716839085064 chr11 135006516 3818309 0.02828240527294253 0.2798890757027377 chr12 133851895 3029098 0.022630221260595527 0.15963208747570187 chr13 115169878 2458908 0.02135027007669488 0.15421596326391634 chr14 107349540 2040335 0.019006462440360715 0.15947832243931234 chr15 102531392 1891585 0.018448837600878374 0.1426919752771306 chr16 90354753 1553634 0.017194823165528436 0.1534618184464813 chr17 81195210 2158488 0.026583932722139644 0.19221383203247633 chr18 78077248 1845338 0.02363477257804988 0.3824549100289862 chr19 59128983 1350030 0.02283195028062634 0.4176943855788812 chr20 63025520 1382432 0.021934479874184298 0.16160204404265993 chr21 48129895 913271 0.018975129698496122 0.15338002938229953 chr22 51304566 742531 0.014473000317359668 0.12587754175388738 chrMT 16571 2027 0.12232212902057812 0.38065059999369366 chrX 155270560 3741640 0.024097549464624845 0.2009179343527856 chrY 59373566 190705 0.003211951257904907 0.09512044617689602