BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524974.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 = 2,537,912 number of mapped reads = 2,344,871 (92.39%) number of supplementary alignments = 5,301 (0.21%) number of secondary alignments = 0 number of mapped bases = 136,461,634 bp number of sequenced bases = 136,418,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,223 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8123 >>>>>>> ACTG content number of A's = 35,100,721 bp (25.73%) number of C's = 25,124,145 bp (18.42%) number of T's = 43,924,858 bp (32.2%) number of G's = 32,266,662 bp (23.65%) number of N's = 1,653 bp (0%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 661,940 number of insertions = 8,721 mapped reads with insertion percentage = 0.37% number of deletions = 25,530 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.07% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.3644X There is a 3.77% of reference with a coverageData >= 1X There is a 0.46% 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 10749445 0.04312705403450128 0.6675328506987228 chr2 243199373 11094645 0.04561954606683957 0.4006742475950412 chr3 198022430 9181538 0.04636615155161968 0.24906143375207487 chr4 191154276 9001688 0.0470912196596638 0.29407930173039426 chr5 180915260 8135096 0.04496633396209916 0.24478749595820667 chr6 171115067 7831222 0.04576582376582888 0.32107012591382744 chr7 159138663 7481235 0.04701079460495405 0.45477827614140487 chr8 146364022 7064724 0.04826817344497407 0.39283934590221314 chr9 141213431 5717121 0.04048567448233731 0.31469826358911607 chr10 135534747 6531966 0.04819403248673936 0.38421296896968754 chr11 135006516 6287781 0.04657390758828263 0.34001965028267384 chr12 133851895 6230445 0.04654730513901204 0.25073253605110835 chr13 115169878 4340557 0.03768830075516794 0.22372000817780505 chr14 107349540 4168963 0.03883540628120065 0.2356942629567244 chr15 102531392 3925000 0.03828095886965038 0.24010375096136957 chr16 90354753 4014181 0.044426893624511375 0.2641466821648594 chr17 81195210 3620685 0.04459234725792322 0.2728646379405421 chr18 78077248 3672351 0.04703484169933858 0.5495496107228346 chr19 59128983 2706658 0.04577548712447836 0.4424609304216206 chr20 63025520 2928900 0.04647165148339911 0.2570551338297794 chr21 48129895 1794453 0.03728354279601067 0.25298537514115227 chr22 51304566 1624445 0.031662776369651 0.20222200977557417 chrMT 16571 6262 0.3778890833383622 0.6602436703143485 chrX 155270560 7941321 0.05114505286771684 0.29276236972787556 chrY 59373566 410952 0.0069214640063896445 0.19402387254254774