BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524542.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 = 2,461,909 number of mapped reads = 2,235,377 (90.8%) number of supplementary alignments = 8,416 (0.34%) number of secondary alignments = 0 number of mapped bases = 129,245,973 bp number of sequenced bases = 129,205,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,526 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9564 >>>>>>> ACTG content number of A's = 32,624,752 bp (25.25%) number of C's = 23,042,533 bp (17.83%) number of T's = 40,505,850 bp (31.35%) number of G's = 33,030,687 bp (25.56%) number of N's = 1,663 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 654,075 number of insertions = 8,234 mapped reads with insertion percentage = 0.37% number of deletions = 24,475 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.3543X There is a 3.67% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10467377 0.041995389853010635 0.6521799435790671 chr2 243199373 11024562 0.04533137509363563 0.416672492467325 chr3 198022430 8507652 0.04296307241558444 0.2351945828495984 chr4 191154276 8322010 0.0435355680978855 0.2625966963475745 chr5 180915260 7776950 0.0429866999610757 0.23254007245825495 chr6 171115067 7349710 0.04295185765260519 0.28262560853017593 chr7 159138663 7112309 0.04469252704479489 0.47570340311763354 chr8 146364022 6619879 0.04522886778828748 0.3144685525601828 chr9 141213431 5270805 0.03732509693075866 0.3031481623886568 chr10 135534747 6224399 0.04592474725318962 0.350703418407474 chr11 135006516 5916048 0.04382046271011097 0.35320345796860897 chr12 133851895 5773679 0.0431348319723079 0.236624797355884 chr13 115169878 3992921 0.03466983788938285 0.20870784180281393 chr14 107349540 3922957 0.03654377093744417 0.2214046567788756 chr15 102531392 3650580 0.03560451027525307 0.22730181040022096 chr16 90354753 3818071 0.04225644886661358 0.2613824534017323 chr17 81195210 3577934 0.044065826050576136 0.2538642155355033 chr18 78077248 3463838 0.0443642429610224 0.5648251620769476 chr19 59128983 2726776 0.04611572636045508 0.48471425373551374 chr20 63025520 2752409 0.04367134138679062 0.2382696258939725 chr21 48129895 1736773 0.036085119238261375 0.23277383559237477 chr22 51304566 1548985 0.030191952115918883 0.1935949284025019 chrMT 16571 23664 1.4280369319896205 1.4563176679269587 chrX 155270560 7265762 0.04679420232657112 0.28163008746564505 chrY 59373566 399923 0.0067357079411400015 0.1835214679709213