BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238328.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 = 1,151,665 number of mapped reads = 1,066,286 (92.59%) number of supplementary alignments = 9,248 (0.8%) number of secondary alignments = 0 number of mapped bases = 72,216,364 bp number of sequenced bases = 72,179,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,585 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8148 >>>>>>> ACTG content number of A's = 20,311,283 bp (28.14%) number of C's = 13,194,175 bp (18.28%) number of T's = 23,050,504 bp (31.93%) number of G's = 15,587,495 bp (21.6%) number of N's = 36,090 bp (0.05%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 581,137 number of insertions = 5,263 mapped reads with insertion percentage = 0.49% number of deletions = 21,104 mapped reads with deletion percentage = 1.96% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2746X There is a 2.1% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7989294 0.0320532561481562 0.5462024851708706 chr2 243199373 4272746 0.01756890220272073 0.2743159105812409 chr3 198022430 4908848 0.024789353408096244 0.1706628775482223 chr4 191154276 4035591 0.021111696188266277 0.16996225819158806 chr5 180915260 5138318 0.02840179429861251 0.18269122596432325 chr6 171115067 4980929 0.029108652366655708 0.2271346331065696 chr7 159138663 3347120 0.021032726660522465 0.2907435356256043 chr8 146364022 3505382 0.02394975180444276 0.39376458475602893 chr9 141213431 2673285 0.018930812608044342 0.24491155430076422 chr10 135534747 3264208 0.024083919970721603 0.27269554659114037 chr11 135006516 2887393 0.021387064014006554 0.2124508345056828 chr12 133851895 3513569 0.026249676928369225 0.17968272838499552 chr13 115169878 1680970 0.014595569858986914 0.12919491655016424 chr14 107349540 1501750 0.01398934732277381 0.14510723229668987 chr15 102531392 1939609 0.018917220981453174 0.14734437954693352 chr16 90354753 2036965 0.02254408243471154 0.18223654222383867 chr17 81195210 1814020 0.022341465709615135 0.1822107749483469 chr18 78077248 2259480 0.028939032277367154 0.44247926258962345 chr19 59128983 1247443 0.021096980477408177 0.38560812065546535 chr20 63025520 1815400 0.028804205026789147 0.1860241102605995 chr21 48129895 671644 0.013954819556535497 0.1558181922897316 chr22 51304566 706150 0.013763882146474058 0.12465237181629155 chrMT 16571 3934 0.2374026914489168 0.5145289625104399 chrX 155270560 5809875 0.03741775002292772 0.23232240068660354 chrY 59373566 212441 0.003578040099528467 0.10249512630417398