BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,981,640 number of mapped reads = 9,387,658 (85.49%) number of secondary alignments = 0 number of mapped bases = 372,532,782 bp number of sequenced bases = 372,492,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 577,721 duplication rate = 4.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2805 >>>>>>> ACTG content number of A's = 109,113,497 bp (29.29%) number of C's = 76,961,885 bp (20.66%) number of T's = 109,785,387 bp (29.47%) number of G's = 76,550,728 bp (20.55%) number of N's = 81,285 bp (0.02%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,248,785 number of insertions = 9,966 mapped reads with insertion percentage = 0.11% number of deletions = 31,402 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.1203X std coverageData = 1.5522X There is a 7.99% of reference with a coverageData >= 1X There is a 2.54% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 30367040 0.1218333574382549 1.5060846023122922 chr2 243199373 31591530 0.129899718121395 0.7524541534102317 chr3 198022430 25618456 0.1293714858463256 0.4970331207933789 chr4 191154276 24787356 0.12967199331706292 0.6363314140563904 chr5 180915260 23296161 0.1287683581805095 0.5097261536578828 chr6 171115067 22020340 0.1286873236007908 0.5285308978086064 chr7 159138663 20737031 0.13030793780138772 0.9937604005061362 chr8 146364022 20122650 0.1374835818600284 6.2303114902932 chr9 141213431 15874763 0.11241680686874607 0.6417829240208689 chr10 135534747 18055531 0.1332169897362187 0.8766397898231867 chr11 135006516 17388306 0.12879605011064799 0.66074305313073 chr12 133851895 16952999 0.12665490466160378 0.5115873295181457 chr13 115169878 12131790 0.10533822046768167 0.4485049977096718 chr14 107349540 11779244 0.10972794107920723 0.544063627776582 chr15 102531392 11122676 0.10848068852903119 0.45053000752468647 chr16 90354753 10590573 0.11721102264537207 0.5336504067276988 chr17 81195210 9756720 0.12016373872301088 0.5158090326656147 chr18 78077248 9958678 0.12754903963828235 1.2091099563849121 chr19 59128983 7085439 0.11983021930209758 1.170033483835844 chr20 63025520 7968346 0.1264304681659112 0.5442556413180867 chr21 48129895 4980020 0.10347041064602364 0.6036818308247287 chr22 51304566 4416150 0.08607713395334053 0.4306483733802035 chrMT 16571 169905 10.253153098787038 12.513506611611342 chrX 155270560 12104732 0.07795896401739003 0.46800635627607806 chrY 59373566 3656346 0.0615820515143052 0.7834705810896774