BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084841.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 = 2,589,902 number of mapped reads = 2,305,980 (89.04%) number of supplementary alignments = 20,656 (0.8%) number of secondary alignments = 0 number of mapped bases = 159,820,856 bp number of sequenced bases = 159,757,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,053 duplication rate = 4.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2362 >>>>>>> ACTG content number of A's = 46,516,750 bp (29.12%) number of C's = 29,064,744 bp (18.19%) number of T's = 51,687,336 bp (32.35%) number of G's = 32,463,702 bp (20.32%) number of N's = 25,308 bp (0.02%) GC percentage = 38.51% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,307,938 number of insertions = 13,231 mapped reads with insertion percentage = 0.57% number of deletions = 35,281 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.449X There is a 4.04% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11595573 0.046521741664988674 0.6431404392451912 chr2 243199373 14137116 0.05812973868152201 0.39796496825870425 chr3 198022430 11238363 0.056752979952826556 0.2895887954189264 chr4 191154276 11219684 0.05869439195804336 0.3084033343778296 chr5 180915260 10063075 0.05562314091138581 0.2900873379899768 chr6 171115067 9473259 0.055361922045123 0.29082082183055274 chr7 159138663 8631922 0.054241513892824396 0.4027949736115918 chr8 146364022 8261403 0.05644421960473319 1.2304131191920127 chr9 141213431 6806852 0.04820258209008462 0.35098414099525427 chr10 135534747 7617821 0.05620566805647263 0.34993029808070647 chr11 135006516 7465286 0.055295745873480656 0.3411134731987869 chr12 133851895 6807468 0.050858211607687734 0.2765631875184148 chr13 115169878 5612408 0.048731561563345585 0.2701381596024511 chr14 107349540 4943475 0.04605026719257484 0.26888261197832247 chr15 102531392 4268737 0.04163346382735153 0.24707409416766665 chr16 90354753 3668327 0.04059915918313672 0.2603224867867464 chr17 81195210 3662425 0.04510641699183979 0.2720253531296655 chr18 78077248 4644837 0.059490275579385174 0.6282723764699002 chr19 59128983 2377477 0.040208318820568925 0.451747365364678 chr20 63025520 2979674 0.047277261655278686 0.2699080096622322 chr21 48129895 2246209 0.04666972574945364 0.27795867103799005 chr22 51304566 1369416 0.026691893271253868 0.19409381097278947 chrMT 16571 256663 15.488685052199626 7.452801951913636 chrX 155270560 10068151 0.0648426269603201 0.3279830310403333 chrY 59373566 405235 0.0068251753650774485 0.14567892346466674