BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237855.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 = 2,153,249 number of mapped reads = 2,050,454 (95.23%) number of supplementary alignments = 11,765 (0.55%) number of secondary alignments = 0 number of mapped bases = 151,864,513 bp number of sequenced bases = 151,785,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,676 duplication rate = 1.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0655 >>>>>>> ACTG content number of A's = 46,342,021 bp (30.53%) number of C's = 30,227,592 bp (19.91%) number of T's = 45,180,416 bp (29.77%) number of G's = 29,772,112 bp (19.61%) number of N's = 263,020 bp (0.17%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,324,112 number of insertions = 11,986 mapped reads with insertion percentage = 0.58% number of deletions = 43,229 mapped reads with deletion percentage = 2.08% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.5659X There is a 3.77% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 20490453 0.08220823249222717 1.338661838911707 chr2 243199373 12396708 0.050973437336945766 0.47967713042850796 chr3 198022430 7674351 0.03875495821357207 0.2574756896208484 chr4 191154276 12227630 0.06396733704246302 0.3541371923584257 chr5 180915260 8809356 0.04869327219826564 0.2766677151109545 chr6 171115067 6314002 0.03689915862289321 0.2627405234015787 chr7 159138663 8638281 0.05428147275561816 0.776710243514541 chr8 146364022 3443270 0.023525385220693102 0.4296031404331237 chr9 141213431 7565980 0.05357833136991056 0.4891285862388667 chr10 135534747 7774577 0.05736224231856942 0.6276995980732974 chr11 135006516 2607940 0.019317141700034686 0.26339117599460865 chr12 133851895 7238128 0.054075648312636886 0.2951523612645411 chr13 115169878 10077678 0.08750272358541528 0.36480506022151243 chr14 107349540 4668020 0.04348430370544671 0.2899667355732357 chr15 102531392 529629 0.005165530182209952 0.08499314043619206 chr16 90354753 2815781 0.031163617922789297 0.30326105461103087 chr17 81195210 4267098 0.05255356812304568 0.39193245216125766 chr18 78077248 3954450 0.05064791730364267 0.8986566094809889 chr19 59128983 855415 0.014466932400985148 0.8494614942807374 chr20 63025520 2921273 0.046350637011800935 0.28829215089751153 chr21 48129895 568674 0.011815400802349559 0.22708165046226333 chr22 51304566 1075295 0.02095905070125727 0.17382918168960856 chrMT 16571 24417 1.473477762355923 1.4309414149351023 chrX 155270560 14448860 0.09305601783106855 0.43029253184677474 chrY 59373566 477247 0.008038038341843912 0.23886819209187102