BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717008.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 = 486,762 number of mapped reads = 436,568 (89.69%) number of supplementary alignments = 1,965 (0.4%) number of secondary alignments = 0 number of mapped bases = 24,858,852 bp number of sequenced bases = 24,851,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,660 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3516 >>>>>>> ACTG content number of A's = 6,103,573 bp (24.56%) number of C's = 4,795,262 bp (19.3%) number of T's = 7,814,773 bp (31.45%) number of G's = 6,137,798 bp (24.7%) number of N's = 496 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 124,422 number of insertions = 1,582 mapped reads with insertion percentage = 0.36% number of deletions = 4,086 mapped reads with deletion percentage = 0.93% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.008X std coverageData = 0.1008X There is a 0.77% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2013780 0.008079337944758822 0.12357956489033255 chr2 243199373 2118268 0.008710006008115818 0.1096183655540123 chr3 198022430 1652294 0.008343973962949551 0.09366437007346069 chr4 191154276 1589580 0.008315691562139054 0.09658461725097933 chr5 180915260 1506855 0.008329065220921663 0.09389990619923333 chr6 171115067 1433373 0.008376661536181381 0.0953858052204968 chr7 159138663 1348384 0.008473013248829419 0.10644377659665007 chr8 146364022 1264842 0.008641754870606111 0.10017939771030696 chr9 141213431 1036971 0.007343288755585862 0.09876309545345235 chr10 135534747 1162496 0.008577106799040987 0.10406440828711731 chr11 135006516 1120096 0.008296606957844909 0.10292229329781624 chr12 133851895 1118176 0.008353830179244006 0.0939138035320791 chr13 115169878 796809 0.006918553825332697 0.0854256784645935 chr14 107349540 745629 0.006945805263813893 0.08721509787089912 chr15 102531392 716680 0.006989859261834658 0.08587328726363537 chr16 90354753 734482 0.008128869546021558 0.09481031174869273 chr17 81195210 686189 0.008451101980030596 0.09605643182714231 chr18 78077248 647393 0.008291698498389698 0.1455128794607686 chr19 59128983 527734 0.008925132366981519 0.11207768583010493 chr20 63025520 539411 0.008558612447783057 0.09628852674563022 chr21 48129895 319656 0.0066415270592217164 0.08635161190134513 chr22 51304566 307284 0.005989408428091956 0.07938849465384154 chrMT 16571 1059 0.06390682517651318 0.2514003592189495 chrX 155270560 1395892 0.008990062250049204 0.10068974145971533 chrY 59373566 75519 0.0012719296664781765 0.04490757042748605