BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004129.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 = 2,159,020 number of mapped reads = 1,338,086 (61.98%) number of supplementary alignments = 8,929 (0.41%) number of secondary alignments = 0 number of mapped bases = 83,854,745 bp number of sequenced bases = 83,812,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,669 duplication rate = 8.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0051 >>>>>>> ACTG content number of A's = 21,545,225 bp (25.71%) number of C's = 15,024,077 bp (17.93%) number of T's = 27,730,761 bp (33.09%) number of G's = 19,502,828 bp (23.27%) number of N's = 9,965 bp (0.01%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 924,489 number of insertions = 7,265 mapped reads with insertion percentage = 0.54% number of deletions = 26,623 mapped reads with deletion percentage = 1.97% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2876X There is a 1.81% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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% 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 7331827 0.02941548137607248 0.3844912787855425 chr2 243199373 7172565 0.029492530805167824 0.3787624176226346 chr3 198022430 5537686 0.02796494316325681 0.23968711665300443 chr4 191154276 5408802 0.028295480034147915 0.24517135007280946 chr5 180915260 4908376 0.027130801459202502 0.23510150134369576 chr6 171115067 5044304 0.029479017180877472 0.2707897214950385 chr7 159138663 4981243 0.03130127466258781 0.3686509371479108 chr8 146364022 5063853 0.03459766225883025 0.336708170528115 chr9 141213431 3057207 0.021649548335101354 0.2471635102962852 chr10 135534747 3917397 0.02890326714521406 0.27959888783053527 chr11 135006516 3565181 0.026407473547424926 0.2721886629962654 chr12 133851895 3417641 0.025533004220821828 0.23553304049802412 chr13 115169878 2467177 0.021422068364090826 0.2137032926667121 chr14 107349540 2296946 0.021396887215352763 0.21639532422569524 chr15 102531392 2316258 0.022590720313248065 0.2159829087891019 chr16 90354753 2314141 0.025611724045109172 0.23536275914305643 chr17 81195210 2105416 0.02593029810502368 0.23502589999013748 chr18 78077248 2418489 0.030975592274973627 0.4077077895196387 chr19 59128983 1500826 0.025382239366437267 0.3211516610699996 chr20 63025520 1954467 0.031010723909933625 0.2611462561110151 chr21 48129895 1174956 0.024412187061700424 0.23016529133453906 chr22 51304566 986018 0.019218913186011554 0.1963336928711118 chrMT 16571 89973 5.429545591696337 4.309932922982551 chrX 155270560 4577858 0.02948310355807308 0.25550685597613193 chrY 59373566 246138 0.004145582227619611 0.10107487849868207