BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524990.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 = 5,294,594 number of mapped reads = 4,919,177 (92.91%) number of supplementary alignments = 10,801 (0.2%) number of secondary alignments = 0 number of mapped bases = 286,418,005 bp number of sequenced bases = 286,326,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 422,341 duplication rate = 6.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8687 >>>>>>> ACTG content number of A's = 71,234,878 bp (24.88%) number of C's = 50,492,309 bp (17.63%) number of T's = 89,582,147 bp (31.29%) number of G's = 75,014,095 bp (26.2%) number of N's = 3,337 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,360,515 number of insertions = 15,350 mapped reads with insertion percentage = 0.31% number of deletions = 53,191 mapped reads with deletion percentage = 1.07% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 0.0925X std coverageData = 0.6829X There is a 7.05% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 23117988 0.09274997152364166 1.3213214666911395 chr2 243199373 24326438 0.10002672992088676 0.7816525727597078 chr3 198022430 19080780 0.09635666020258413 0.4016611749586203 chr4 191154276 18435885 0.09644505676660876 0.5155283547662008 chr5 180915260 17297969 0.09561365359671704 0.39775448673618985 chr6 171115067 16796824 0.09816098777555339 0.5944987254029572 chr7 159138663 15781512 0.0991683083324635 0.8817978499035471 chr8 146364022 14648617 0.10008345493539389 0.7238532436040319 chr9 141213431 11963999 0.08472281223731473 0.5727817480888324 chr10 135534747 13989903 0.10322004732852749 0.7451573820175527 chr11 135006516 13148120 0.09738878084965914 0.66789801541739 chr12 133851895 12924618 0.09655909615624045 0.4094316954442446 chr13 115169878 8978138 0.07795560919149364 0.3592008261180641 chr14 107349540 8652182 0.08059822147351539 0.39339121988107095 chr15 102531392 8017572 0.07819626597871605 0.40058877223269557 chr16 90354753 8322012 0.09210375463037346 0.44506383836705166 chr17 81195210 7606883 0.09368635169488447 0.4904566611271586 chr18 78077248 7667019 0.098197864248494 1.0383394267357826 chr19 59128983 5646644 0.09549705936934515 0.8293012684720261 chr20 63025520 6073237 0.09636155322478894 0.41516971058012153 chr21 48129895 3774487 0.07842292196980692 0.45372505134928875 chr22 51304566 3350966 0.06531516122756013 0.3236781034999404 chrMT 16571 9352 0.5643594230885282 0.873453636308503 chrX 155270560 15941428 0.10266870938058058 0.49438466934806863 chrY 59373566 865432 0.01457604887670045 0.3787482078171588