BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714161.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 779,886 number of mapped reads = 682,218 (87.48%) number of supplementary alignments = 3,789 (0.49%) number of secondary alignments = 0 number of mapped bases = 84,735,644 bp number of sequenced bases = 84,535,674 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 671,387 duplication rate = 31.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 13.873 >>>>>>> ACTG content number of A's = 25,089,234 bp (29.68%) number of C's = 16,958,866 bp (20.06%) number of T's = 23,181,806 bp (27.42%) number of G's = 19,305,187 bp (22.84%) number of N's = 581 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0366 number of mismatches = 2,113,491 number of insertions = 272,003 mapped reads with insertion percentage = 39.17% number of deletions = 56,691 mapped reads with deletion percentage = 8.08% homopolymer indels = 14.18% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 92.3444X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 5276959 0.021171297302404714 22.248059096318112 chr2 243199373 1348407 0.005544450971919241 5.280067765962763 chr3 198022430 10699156 0.05403002074057974 62.61923247715468 chr4 191154276 57618 3.014214549927201E-4 0.05262683819199294 chr5 180915260 64261852 0.35520415469651373 375.32291696174485 chr6 171115067 77672 4.539167787019012E-4 0.2725653030706397 chr7 159138663 971497 0.006104720133284015 5.717632773847498 chr8 146364022 65620 4.4833422246349586E-4 0.18381005815870166 chr9 141213431 69184 4.899250695211846E-4 0.2830332750380393 chr10 135534747 71710 5.290894149822702E-4 0.2575776610577727 chr11 135006516 118403 8.770169285755066E-4 0.21199433987827757 chr12 133851895 174758 0.001305607216095073 0.8101595080340859 chr13 115169878 63351 5.500657038118943E-4 0.3592618685028101 chr14 107349540 26779 2.49456122494796E-4 0.05814865452899165 chr15 102531392 427945 0.004173794890056696 0.7700983027950515 chr16 90354753 43983 4.867812543298082E-4 0.24930061113052276 chr17 81195210 23110 2.8462270126525935E-4 0.04834548857016188 chr18 78077248 25384 3.251139179495671E-4 0.0926591181721915 chr19 59128983 141044 0.0023853615070632958 0.5248253132316225 chr20 63025520 17483 2.77395569286854E-4 0.04460433151474458 chr21 48129895 13953 2.899029802579042E-4 0.0777137463727624 chr22 51304566 10128 1.9740932999998478E-4 0.04210909073804569 chrMT 16571 8401 0.5069700078450304 3.8253324888587437 chrX 155270560 724463 0.004665810440820204 2.934258730597594 chrY 59373566 16784 2.8268472201922317E-4 0.12497327077456048