BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082421.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,476,644 number of mapped reads = 3,126,221 (89.92%) number of supplementary alignments = 27,482 (0.79%) number of secondary alignments = 0 number of mapped bases = 210,856,385 bp number of sequenced bases = 210,783,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 137,937 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3712 >>>>>>> ACTG content number of A's = 58,994,193 bp (27.99%) number of C's = 39,117,574 bp (18.56%) number of T's = 66,194,241 bp (31.4%) number of G's = 46,472,957 bp (22.05%) number of N's = 4,302 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,708,961 number of insertions = 16,587 mapped reads with insertion percentage = 0.53% number of deletions = 45,642 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0681X std coverageData = 0.4989X There is a 5.68% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.03% 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% 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 16448124 0.06599030298905453 0.765956168577446 chr2 243199373 18225434 0.07494030011335596 0.6474458117991067 chr3 198022430 14686004 0.07416333594128706 0.31420627598202844 chr4 191154276 14155442 0.0740524475633493 0.3251305325644966 chr5 180915260 13299556 0.07351262685082507 0.31485122412945266 chr6 171115067 12163277 0.0710824430206371 0.3701782726884927 chr7 159138663 11555677 0.0726138876760577 0.6273844654821449 chr8 146364022 10899540 0.07446871062343449 0.9461241551604425 chr9 141213431 8822270 0.06247472310194064 0.4466392883071644 chr10 135534747 9900408 0.07304700985644663 0.42490917700257747 chr11 135006516 9620767 0.07126150118561685 0.42185829926449886 chr12 133851895 9570830 0.07150313411700297 0.3144075186279742 chr13 115169878 6732026 0.05845300973575747 0.27905865382908723 chr14 107349540 6386084 0.059488694595244654 0.29857751054936 chr15 102531392 6093338 0.05942899907181597 0.2949695425459237 chr16 90354753 5771004 0.06387050828416298 0.32277168402863565 chr17 81195210 5220934 0.0643010098748436 0.32680988780587905 chr18 78077248 5842660 0.0748317871039717 0.8309655484986841 chr19 59128983 3773382 0.06381611535581459 0.6223468231173255 chr20 63025520 3995785 0.06339947691030554 0.3012799268627545 chr21 48129895 2788448 0.05793588371634719 0.2949145580463598 chr22 51304566 2069802 0.040343426742953055 0.22999183922464697 chrMT 16571 3145 0.18978939110494236 0.45470155819926866 chrX 155270560 12346586 0.07951659348687865 0.36534454648756215 chrY 59373566 485862 0.008183136583037643 0.15587874538445748