BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083657.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 = 1,527,871 number of mapped reads = 1,255,608 (82.18%) number of supplementary alignments = 8,475 (0.55%) number of secondary alignments = 0 number of mapped bases = 78,660,720 bp number of sequenced bases = 78,633,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,106 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6974 >>>>>>> ACTG content number of A's = 23,586,325 bp (30%) number of C's = 15,047,909 bp (19.14%) number of T's = 22,924,992 bp (29.15%) number of G's = 17,068,887 bp (21.71%) number of N's = 5,096 bp (0.01%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 670,657 number of insertions = 5,781 mapped reads with insertion percentage = 0.46% number of deletions = 17,029 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.3385X There is a 2.32% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 6113410 0.024527160556201785 0.9137930281956432 chr2 243199373 9754083 0.04010735257939995 0.255249573011818 chr3 198022430 1143458 0.005774386265232681 0.08398741146138552 chr4 191154276 2784027 0.014564293607536145 0.12799899007774573 chr5 180915260 717893 0.003968117449020055 0.07243540158794783 chr6 171115067 4362038 0.025491840528572507 0.18732392507239082 chr7 159138663 5575784 0.03503726809618854 0.44032668873720937 chr8 146364022 6711282 0.045853358689473565 0.2662494549746905 chr9 141213431 4334769 0.030696577296532083 0.21630339179255914 chr10 135534747 4578441 0.03378056993753786 0.23802790283878988 chr11 135006516 3336783 0.024715718165780977 0.20817803555972642 chr12 133851895 3229214 0.024125276672399745 0.1646819248058098 chr13 115169878 1884910 0.01636634537374434 0.1344594967970671 chr14 107349540 3519125 0.03278192901432088 0.19388623587235937 chr15 102531392 2992539 0.029186563662375715 0.18063699829959742 chr16 90354753 3248115 0.03594846858803322 0.2106988836536204 chr17 81195210 2105119 0.025926640253778516 0.17969969050868576 chr18 78077248 2043383 0.026171298967914442 0.3645889424864395 chr19 59128983 3050646 0.05159307407671801 0.5549287333445138 chr20 63025520 881748 0.013990332804870154 0.12672954812611384 chr21 48129895 539854 0.011216604565623923 0.11316647842917787 chr22 51304566 127422 0.002483638590764027 0.0718887760376977 chrMT 16571 3304 0.19938446683965966 0.50519202313604 chrX 155270560 5442655 0.03505271701216251 0.20974738556431646 chrY 59373566 180718 0.00304374509019721 0.06913265184055631