BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238293.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 = 2,686,897 number of mapped reads = 2,407,922 (89.62%) number of supplementary alignments = 22,457 (0.84%) number of secondary alignments = 0 number of mapped bases = 156,535,945 bp number of sequenced bases = 156,462,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,545 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0609 >>>>>>> ACTG content number of A's = 42,967,602 bp (27.46%) number of C's = 30,563,342 bp (19.53%) number of T's = 46,555,767 bp (29.76%) number of G's = 36,338,540 bp (23.23%) number of N's = 37,344 bp (0.02%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,391,593 number of insertions = 13,468 mapped reads with insertion percentage = 0.55% number of deletions = 44,042 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.5156X There is a 4.38% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 17639506 0.07077015868297476 1.0343629400738696 chr2 243199373 12449749 0.05119153411633179 0.6809715254153972 chr3 198022430 8493501 0.04289161081398708 0.23533131939781704 chr4 191154276 8176490 0.04277429817996852 0.2623906881478757 chr5 180915260 11742454 0.06490582386471987 0.2906382773104196 chr6 171115067 5432277 0.03174633943836167 0.230558170399602 chr7 159138663 6553788 0.04118287709882293 0.5240628712169444 chr8 146364022 6876116 0.0469795507532582 0.5884586626855459 chr9 141213431 7459759 0.052826129548541316 0.5728463888245654 chr10 135534747 7750288 0.05718303366147133 0.47191951796325476 chr11 135006516 6182076 0.04579094537925858 0.41470967675099946 chr12 133851895 5884692 0.04396420386876106 0.25285495893586046 chr13 115169878 3088865 0.02682007703437873 0.1821528853753156 chr14 107349540 4437788 0.04133960890749974 0.32827949528110495 chr15 102531392 5169620 0.05041987530999287 0.25665735484176244 chr16 90354753 4829889 0.05345473082085676 0.3369662046384056 chr17 81195210 4954453 0.06101903055611285 0.3301926739948806 chr18 78077248 4276426 0.05477173068395034 0.9954131909537768 chr19 59128983 3686143 0.06234071369027267 0.7566512590666841 chr20 63025520 4371962 0.06936812262715167 0.30734653401844636 chr21 48129895 1985587 0.0412547544514693 0.2803894759353939 chr22 51304566 2840173 0.055359068820502254 0.26536026026298126 chrMT 16571 10683 0.6446804658741174 0.9584567393716917 chrX 155270560 11740314 0.07561197692595428 0.3884579411454924 chrY 59373566 503346 0.008477611063482358 0.20833170085517796