BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 17,356,496 number of mapped reads = 14,100,743 (81.24%) number of supplementary alignments = 256 (0%) number of secondary alignments = 0 number of mapped bases = 703,228,157 bp number of sequenced bases = 703,173,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,251 duplication rate = 0.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1689 >>>>>>> ACTG content number of A's = 217,459,953 bp (30.93%) number of C's = 133,675,866 bp (19.01%) number of T's = 215,730,546 bp (30.68%) number of G's = 136,291,817 bp (19.38%) number of N's = 15,150 bp (0%) GC percentage = 38.39% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,433,864 number of insertions = 45,368 mapped reads with insertion percentage = 0.32% number of deletions = 33,614 mapped reads with deletion percentage = 0.24% homopolymer indels = 49.46% >>>>>>> Coverage mean coverageData = 0.2272X std coverageData = 0.5209X There is a 18.71% of reference with a coverageData >= 1X There is a 3.35% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.09% 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 54149165 0.2172478639481504 0.514262864653639 chr2 243199373 67029111 0.2756138314550671 0.567031856284003 chr3 198022430 57433240 0.2900340128135989 0.5800139669108288 chr4 191154276 57829978 0.30253039173447527 0.5895820257328568 chr5 180915260 51386746 0.28403765387176294 0.5730524259251183 chr6 171115067 47713040 0.2788359951961448 0.5696253969928997 chr7 159138663 40598224 0.2551122601802932 0.5515383156732848 chr8 146364022 39815835 0.2720329385318477 0.5617190170673457 chr9 141213431 29550793 0.209263331332839 0.5054044459884576 chr10 135534747 30144101 0.22240865657867057 0.506856188592432 chr11 135006516 31872788 0.23608333097048442 0.5279459850731579 chr12 133851895 32175442 0.2403809225114071 0.5334947703631039 chr13 115169878 30529892 0.2650857370883036 0.5639097707438882 chr14 107349540 21907215 0.2040736737204463 0.49644161625437266 chr15 102531392 18295597 0.17843897993699334 0.46501352327485485 chr16 90354753 11812017 0.13072933750369503 0.39340118384984285 chr17 81195210 9478314 0.11673489113458786 0.37363662062487335 chr18 78077248 22345995 0.2862036710105356 0.5782135979398753 chr19 59128983 3547468 0.05999541713748061 0.25981784026242605 chr20 63025520 11099088 0.17610466363466734 0.4599341478335861 chr21 48129895 9133944 0.18977693593555522 0.4881857990768457 chr22 51304566 2927370 0.057058664135274044 0.2553072564485837 chrMT 16571 1695 0.10228712811538229 0.3114711237472819 chrX 155270560 19722832 0.1270223537546332 0.3709385919106686 chrY 59373566 2728267 0.04595086978605934 0.22998390838214605