BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818843.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 774,496 number of mapped reads = 764,497 (98.71%) number of supplementary alignments = 10,569 (1.36%) number of secondary alignments = 0 number of mapped bases = 70,826,823 bp number of sequenced bases = 70,783,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,432 duplication rate = 10.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2778 >>>>>>> ACTG content number of A's = 19,628,144 bp (27.73%) number of C's = 15,293,496 bp (21.61%) number of T's = 19,875,404 bp (28.08%) number of G's = 15,985,705 bp (22.58%) number of N's = 1,030 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 420,929 number of insertions = 8,344 mapped reads with insertion percentage = 1.05% number of deletions = 22,102 mapped reads with deletion percentage = 2.82% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.2964X There is a 1.86% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 6277045 0.025183668449114918 0.42451848952483834 chr2 243199373 5308951 0.021829624536079704 0.36819995888375684 chr3 198022430 4450869 0.0224765901519338 0.1740170130626147 chr4 191154276 3621115 0.018943416154603834 0.20123839553085413 chr5 180915260 3111158 0.01719676936041769 0.1578669995880561 chr6 171115067 3558825 0.020797847100162137 0.17912946288287465 chr7 159138663 6322008 0.03972641142523611 0.621963711248427 chr8 146364022 6127262 0.04186317044498818 0.2815921667486565 chr9 141213431 2669030 0.018900680913276586 0.26322365741125686 chr10 135534747 3280805 0.024206375653617444 0.4043183466699148 chr11 135006516 3207645 0.023759186556595535 0.20445202861428685 chr12 133851895 2813887 0.021022391950446424 0.17020937579257667 chr13 115169878 2143205 0.01860907589048588 0.1575110477297452 chr14 107349540 2109743 0.019653023198795264 0.1710451004529524 chr15 102531392 1996014 0.019467345181464035 0.16454424051699454 chr16 90354753 1952274 0.021606765944011824 0.27600853801769765 chr17 81195210 1802659 0.02220154366248945 0.20620315742948273 chr18 78077248 1056063 0.013525873760304667 0.2809698781687306 chr19 59128983 1296699 0.0219300068123952 0.39913242092989587 chr20 63025520 3049770 0.04838944605296394 0.2708044116287861 chr21 48129895 667292 0.013864397584910584 0.16266606614886667 chr22 51304566 650422 0.012677663036853288 0.13738140632417262 chrMT 16571 197325 11.907851065113753 8.236425682680908 chrX 155270560 2894107 0.018639122574169886 0.17969643312528005 chrY 59373566 262650 0.004423685786364929 0.3043818644793286