BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504707.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,223,752 number of mapped reads = 2,007,040 (90.25%) number of secondary alignments = 0 number of mapped bases = 64,218,844 bp number of sequenced bases = 64,218,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 374,376 duplication rate = 11.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.5079 >>>>>>> ACTG content number of A's = 18,621,589 bp (29%) number of C's = 12,832,169 bp (19.98%) number of T's = 19,914,548 bp (31.01%) number of G's = 12,850,458 bp (20.01%) number of N's = 80 bp (0%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0004 number of mismatches = 28,043 >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.7252X There is a 0.99% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 3602710 0.014454166595637087 0.3172338526806694 chr2 243199373 10776390 0.044310928383849084 1.8351779140477733 chr3 198022430 5496198 0.027755431543790267 0.9457893785649562 chr4 191154276 4509322 0.023589961440360352 0.38063062725488495 chr5 180915260 6350410 0.035101571862981594 1.3554400081647313 chr6 171115067 2532140 0.014797878669562161 0.2547910017012589 chr7 159138663 2257796 0.014187601915444017 0.2094045298288777 chr8 146364022 4051062 0.027677990428549442 0.5746771047231014 chr9 141213431 2704018 0.019148447713872203 0.4353039153510077 chr10 135534747 2213638 0.016332623544868533 0.3042113491212303 chr11 135006516 3380616 0.025040391383775878 0.48036141104022045 chr12 133851895 2807640 0.020975720963830956 0.3273522748325021 chr13 115169878 2084894 0.018102771629227566 0.4205419461741955 chr14 107349540 1865728 0.01737993474401474 0.3046255492406199 chr15 102531392 1940746 0.018928310268137197 0.5535207129356484 chr16 90354753 1245968 0.013789733894795772 0.2294367933842235 chr17 81195210 876116 0.010790242429325572 0.18595394209479588 chr18 78077248 1640906 0.02101644258773055 0.35356353360833026 chr19 59128983 735948 0.012446485000426949 0.2185294625770334 chr20 63025520 590410 0.009367792602107844 0.13398217403107637 chr21 48129895 512876 0.01065607976082225 0.17829513804279304 chr22 51304566 547504 0.01067164275398022 0.2432482052528912 chrMT 16571 0 0.0 0.0 chrX 155270560 917114 0.0059065543397280205 0.10163800580186201 chrY 59373566 578694 0.009746660660402308 0.3205724625113195