BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717041.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 = 4,169,242 number of mapped reads = 3,608,989 (86.56%) number of supplementary alignments = 82,264 (1.97%) number of secondary alignments = 0 number of mapped bases = 273,101,335 bp number of sequenced bases = 273,003,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,027 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.966 >>>>>>> ACTG content number of A's = 71,173,175 bp (26.07%) number of C's = 54,867,169 bp (20.1%) number of T's = 83,071,399 bp (30.43%) number of G's = 63,858,436 bp (23.39%) number of N's = 33,248 bp (0.01%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,968,720 number of insertions = 21,938 mapped reads with insertion percentage = 0.6% number of deletions = 57,562 mapped reads with deletion percentage = 1.57% homopolymer indels = 41.66% >>>>>>> Coverage mean coverageData = 0.0882X std coverageData = 0.7213X There is a 6.8% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23381528 0.09380730088532056 1.0077214582376282 chr2 243199373 18483466 0.07600128969082498 1.1004253056769033 chr3 198022430 21910516 0.11064663735315237 0.44191183544211315 chr4 191154276 12638451 0.06611649639477592 0.34739534024672214 chr5 180915260 18217276 0.1006950768000444 0.4155861583017519 chr6 171115067 20787610 0.12148322391738887 0.5293717097009999 chr7 159138663 15458570 0.09713899632297401 1.3234658117386457 chr8 146364022 19208796 0.13123987532947134 0.8373752059448726 chr9 141213431 11448659 0.08107344265291593 0.6240770246808289 chr10 135534747 14281240 0.1053695846718923 0.6530386571081962 chr11 135006516 11403344 0.08446513796415575 0.5516839663784625 chr12 133851895 11006844 0.08223151416720698 0.3663151262034399 chr13 115169878 10324588 0.0896466001292456 0.3702944045219303 chr14 107349540 6660312 0.06204322813120578 0.38394753206294824 chr15 102531392 4299389 0.041932416171624784 0.2544765998618893 chr16 90354753 6729129 0.07447454369113267 0.42176627660474286 chr17 81195210 7767261 0.09566156673527909 0.45031937022842294 chr18 78077248 8779087 0.11244104044240903 1.5246107024869266 chr19 59128983 4693849 0.07938321888607487 0.8712014883033747 chr20 63025520 5038661 0.07994636141042549 0.46575662483051455 chr21 48129895 6881387 0.14297531710800532 0.5151159158460631 chr22 51304566 3885535 0.0757346821723431 0.34428955882196427 chrMT 16571 163744 9.88135900066381 7.626243570732657 chrX 155270560 9097779 0.05859307134591387 0.4524772069026638 chrY 59373566 554314 0.009336040216954462 0.23117352542121453