BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068073.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 = 3,511,107 number of mapped reads = 3,123,697 (88.97%) number of supplementary alignments = 26,455 (0.75%) number of secondary alignments = 0 number of mapped bases = 200,357,082 bp number of sequenced bases = 200,280,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 463,303 duplication rate = 12.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4051 >>>>>>> ACTG content number of A's = 51,911,821 bp (25.92%) number of C's = 36,378,066 bp (18.16%) number of T's = 64,815,880 bp (32.36%) number of G's = 47,151,356 bp (23.54%) number of N's = 23,005 bp (0.01%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,094,483 number of insertions = 13,347 mapped reads with insertion percentage = 0.42% number of deletions = 43,993 mapped reads with deletion percentage = 1.39% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.0647X std coverageData = 0.6713X There is a 4.46% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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% 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 23479637 0.09420091675518835 1.17041793116337 chr2 243199373 18808659 0.07733843540789063 1.2434599112192886 chr3 198022430 13220554 0.06676291165601796 0.35412515157905833 chr4 191154276 10061492 0.05263545347005473 0.3589992695815093 chr5 180915260 9528715 0.05266949288854904 0.3182651655036871 chr6 171115067 12707487 0.07426281754604344 0.50832445649611 chr7 159138663 15250943 0.09583430394912894 0.8821782846970057 chr8 146364022 6585574 0.0449944864182538 0.76740391991934 chr9 141213431 6126195 0.04338252357879471 0.4928547525438392 chr10 135534747 9855385 0.07271482197845545 0.5028758402460858 chr11 135006516 10334420 0.07654756456347633 0.51793668838357 chr12 133851895 7100691 0.05304886419426486 0.3398664267090881 chr13 115169878 5077433 0.04408646677562687 0.32596453581615936 chr14 107349540 4610714 0.04295047747759329 0.32853873602365535 chr15 102531392 3626071 0.03536547128902727 0.2836420864574072 chr16 90354753 4778412 0.05288500982344559 0.3427980126099829 chr17 81195210 5867906 0.07226911538254535 0.404066848302636 chr18 78077248 6097949 0.07810148482692422 0.9689236561052819 chr19 59128983 3137851 0.05306790072814207 0.7988932605331087 chr20 63025520 3390515 0.05379590680092763 0.3492087320785726 chr21 48129895 3415051 0.07095488157620124 0.38794467890442924 chr22 51304566 2383884 0.046465337997401636 0.2892891523747232 chrMT 16571 235001 14.181461589523867 9.868831174047132 chrX 155270560 14013406 0.0902515325506651 0.47900218422606167 chrY 59373566 663137 0.01116889290429347 0.35674190877767287