BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237324.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,752,156 number of mapped reads = 2,539,017 (92.26%) number of supplementary alignments = 28,511 (1.04%) number of secondary alignments = 0 number of mapped bases = 157,472,991 bp number of sequenced bases = 157,403,663 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 589,543 duplication rate = 18.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0293 >>>>>>> ACTG content number of A's = 40,949,861 bp (26.02%) number of C's = 27,095,343 bp (17.21%) number of T's = 52,743,504 bp (33.51%) number of G's = 36,598,254 bp (23.25%) number of N's = 16,701 bp (0.01%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 852,421 number of insertions = 10,580 mapped reads with insertion percentage = 0.41% number of deletions = 40,359 mapped reads with deletion percentage = 1.57% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.6479X There is a 2.74% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 22392314 0.08983854848650508 0.8576326655930817 chr2 243199373 7717214 0.031732047269710684 1.3459226780551554 chr3 198022430 12460483 0.0629246040461174 0.4182798525562352 chr4 191154276 9828135 0.051414675128690294 0.40588290668532473 chr5 180915260 8635722 0.04773351899668386 0.36817690337662595 chr6 171115067 20493955 0.11976709800779846 0.8579727550768605 chr7 159138663 9721005 0.06108512423533431 0.462522306207033 chr8 146364022 12230550 0.08356254380601812 0.723644461765819 chr9 141213431 4834158 0.03423299020331855 0.32762860274394706 chr10 135534747 5359972 0.03954684771721306 0.4300264902651641 chr11 135006516 4645006 0.034405791198996644 0.326418800714118 chr12 133851895 4240742 0.03168234562536451 0.2996397411158463 chr13 115169878 6021270 0.05228163912789766 0.4477902395883871 chr14 107349540 2157179 0.020094906787676968 0.23887798719667147 chr15 102531392 2634987 0.025699319482563935 0.33023005485502327 chr16 90354753 2756880 0.03051173190634476 0.3189784458559693 chr17 81195210 4416314 0.05439131199980886 0.395828359166197 chr18 78077248 2127350 0.027246733901276847 1.4346154393889823 chr19 59128983 2779929 0.04701465946065739 0.5685152477028427 chr20 63025520 1332264 0.021138484855023808 0.23990795869917494 chr21 48129895 1784255 0.03707165785422968 0.3407728916705331 chr22 51304566 1095275 0.021348489723117432 0.23050358874175136 chrMT 16571 69206 4.17633214652103 5.037326100095397 chrX 155270560 7320031 0.047143714816253644 0.3674124084399485 chrY 59373566 418795 0.007053559828291264 0.25835318092734616