BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085139.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 = 2,458,780 number of mapped reads = 2,241,392 (91.16%) number of supplementary alignments = 22,581 (0.92%) number of secondary alignments = 0 number of mapped bases = 152,248,850 bp number of sequenced bases = 152,190,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,921 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7635 >>>>>>> ACTG content number of A's = 43,206,672 bp (28.39%) number of C's = 28,211,940 bp (18.54%) number of T's = 47,842,883 bp (31.44%) number of G's = 32,900,693 bp (21.62%) number of N's = 28,458 bp (0.02%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,349,805 number of insertions = 12,018 mapped reads with insertion percentage = 0.53% number of deletions = 35,855 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.424X There is a 4.33% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 12032508 0.04827473629443836 0.7805910966089746 chr2 243199373 13286570 0.05463241880973106 0.4789861471870526 chr3 198022430 10165940 0.051337315676814994 0.2490798260593205 chr4 191154276 10031909 0.052480693657096116 0.26173772494317404 chr5 180915260 9593198 0.05302591942769228 0.2545831532895389 chr6 171115067 8764400 0.05121933534935296 0.28914891879959703 chr7 159138663 8662028 0.05443069482115732 0.5541622370875007 chr8 146364022 8041137 0.05493930058850118 0.7171379824212676 chr9 141213431 6311142 0.04469222194594224 0.369346565077116 chr10 135534747 7230771 0.05334994280101471 0.3826148954870678 chr11 135006516 6909155 0.05117645580899221 0.35820873416147136 chr12 133851895 6864634 0.05128529558733554 0.2522999854080951 chr13 115169878 5016730 0.043559393194807415 0.22991739986330278 chr14 107349540 4615787 0.0429977343172593 0.24147472595116398 chr15 102531392 4333965 0.04226963972165715 0.23343699957658143 chr16 90354753 4088712 0.04525176445338742 0.25853361797250735 chr17 81195210 3785204 0.04661856284379337 0.26305362224842394 chr18 78077248 4152189 0.053180524497994604 0.6920172079595676 chr19 59128983 2739065 0.0463235601397034 0.5590577440963943 chr20 63025520 2982562 0.04732308436328649 0.24402649809011923 chr21 48129895 1962550 0.04077611222713035 0.2367059495966621 chr22 51304566 1523321 0.029691723734686693 0.18662292822372606 chrMT 16571 9361 0.5649025405829461 0.804969041632894 chrX 155270560 8782917 0.05656524327599514 0.29489628807057333 chrY 59373566 363095 0.006115431907862835 0.13182782153570244