BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818980.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 = 689,213 number of mapped reads = 678,387 (98.43%) number of supplementary alignments = 9,707 (1.41%) number of secondary alignments = 0 number of mapped bases = 62,841,251 bp number of sequenced bases = 62,804,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 202,074 duplication rate = 24.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2988 >>>>>>> ACTG content number of A's = 18,335,878 bp (29.19%) number of C's = 13,774,648 bp (21.93%) number of T's = 17,720,682 bp (28.22%) number of G's = 12,970,343 bp (20.65%) number of N's = 3,336 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 397,008 number of insertions = 8,878 mapped reads with insertion percentage = 1.27% number of deletions = 19,971 mapped reads with deletion percentage = 2.88% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0203X std coverageData = 0.282X There is a 1.29% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6438518 0.0258315023415729 0.47538494943256765 chr2 243199373 5122656 0.02106360693619058 0.36535231992013345 chr3 198022430 3439204 0.017367749703909804 0.1935608260439729 chr4 191154276 3549942 0.01857108339025594 0.21720002953292358 chr5 180915260 3482952 0.01925184199497599 0.20838913592443808 chr6 171115067 2609940 0.015252543482918428 0.19856634051764457 chr7 159138663 2785373 0.017502805085147663 0.2988011512464154 chr8 146364022 5865116 0.040072115536699315 0.31185957570564693 chr9 141213431 2737569 0.01938603842859678 0.26065566884990926 chr10 135534747 3317941 0.024480371811960513 0.3244605715924009 chr11 135006516 2106583 0.015603565386429201 0.20168200894810753 chr12 133851895 2863409 0.02139236803483432 0.21881516758596534 chr13 115169878 1332350 0.011568563092512784 0.15876026176500527 chr14 107349540 1472748 0.013719183146942223 0.17811918643248476 chr15 102531392 1638761 0.015983017181703727 0.19402514215521097 chr16 90354753 2040483 0.02258301785186663 0.31920786809531476 chr17 81195210 2177542 0.026818601737713346 0.2602354004260017 chr18 78077248 1441951 0.018468261073955886 0.27188402112026355 chr19 59128983 1332341 0.0225327907297171 0.41298957528325436 chr20 63025520 1651631 0.02620574967092695 0.2547919676262279 chr21 48129895 872675 0.018131662244432488 0.21249947943714587 chr22 51304566 483307 0.009420350617525934 0.1530360301187647 chrMT 16571 7360 0.4441494176573532 1.2180309402245848 chrX 155270560 3830352 0.024668887650047763 0.24597756788432423 chrY 59373566 240547 0.004051415742824004 0.27336167125030786