BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717035.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 = 2,328,487 number of mapped reads = 1,958,268 (84.1%) number of supplementary alignments = 44,474 (1.91%) number of secondary alignments = 0 number of mapped bases = 148,289,510 bp number of sequenced bases = 148,233,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,948 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4361 >>>>>>> ACTG content number of A's = 38,625,471 bp (26.06%) number of C's = 28,575,556 bp (19.28%) number of T's = 44,997,516 bp (30.36%) number of G's = 36,016,587 bp (24.3%) number of N's = 18,853 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,107,750 number of insertions = 12,513 mapped reads with insertion percentage = 0.63% number of deletions = 32,230 mapped reads with deletion percentage = 1.62% homopolymer indels = 41.13% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.4275X There is a 4.13% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 12840490 0.051516381176839675 0.6200151283307329 chr2 243199373 10496452 0.0431598645609995 0.6745350392430514 chr3 198022430 11829876 0.059740080959515544 0.27856443591513397 chr4 191154276 7167207 0.03749435874507981 0.22724352501942802 chr5 180915260 9721769 0.05373658916334642 0.26467744025377715 chr6 171115067 11115938 0.06496177218573043 0.33308427512773364 chr7 159138663 7795523 0.04898572636619424 0.6528220607843337 chr8 146364022 9556067 0.06528972673352745 0.5560079166938651 chr9 141213431 5478607 0.03879664250916756 0.3978087995662021 chr10 135534747 7572027 0.055867791600334046 0.37778774720332614 chr11 135006516 6348893 0.047026567221392486 0.3505788820914007 chr12 133851895 6114421 0.04568049634261809 0.24356952713961513 chr13 115169878 5036962 0.04373506412848679 0.23294765838927256 chr14 107349540 3760857 0.035033750493947156 0.24112937355979316 chr15 102531392 3165218 0.03087072103731899 0.19638157115485425 chr16 90354753 3882396 0.04296836492929154 0.26847656455753793 chr17 81195210 4784707 0.05892843925152728 0.3124836991755219 chr18 78077248 4791395 0.06136736530467877 0.7909972143711802 chr19 59128983 2763002 0.0467283869908603 0.5417210181800158 chr20 63025520 2953520 0.046862286895847906 0.2828665434019613 chr21 48129895 3296319 0.0684879740543793 0.30901470854068835 chr22 51304566 2463463 0.048016447502937654 0.252447983314357 chrMT 16571 21784 1.3145857220445356 1.6311394215772508 chrX 155270560 5032053 0.032408287829965965 0.26664419682676127 chrY 59373566 300564 0.005062252787713643 0.15904829153343436