BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080957.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 = 4,622,842 number of mapped reads = 4,185,417 (90.54%) number of supplementary alignments = 52,962 (1.15%) number of secondary alignments = 0 number of mapped bases = 289,639,163 bp number of sequenced bases = 289,531,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,293 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5659 >>>>>>> ACTG content number of A's = 84,124,690 bp (29.06%) number of C's = 51,763,122 bp (17.88%) number of T's = 92,114,630 bp (31.82%) number of G's = 60,112,738 bp (20.76%) number of N's = 1,415,839 bp (0.49%) GC percentage = 38.64% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 3,331,021 number of insertions = 22,450 mapped reads with insertion percentage = 0.53% number of deletions = 65,345 mapped reads with deletion percentage = 1.54% homopolymer indels = 49.69% >>>>>>> Coverage mean coverageData = 0.0936X std coverageData = 0.6816X There is a 6.56% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 23586082 0.09462797687472964 1.1067177897575642 chr2 243199373 19333532 0.079496635873317 0.5742620644101587 chr3 198022430 25790041 0.13023797859666705 0.4826660059588475 chr4 191154276 18381601 0.09616107672108784 0.43840942952360856 chr5 180915260 16936845 0.0936175588504806 0.40858708809885674 chr6 171115067 24848290 0.1452139220446321 0.7590661395164203 chr7 159138663 14278833 0.0897257318292287 0.5957709524404118 chr8 146364022 22426832 0.15322639876622138 1.4508242031738827 chr9 141213431 14872829 0.10532163190624552 0.7395182084746204 chr10 135534747 12917356 0.09530660060183681 0.5697946822090552 chr11 135006516 13199645 0.09777042909543714 0.4896011845791231 chr12 133851895 14300054 0.10683490136617042 0.4571212015510847 chr13 115169878 7937726 0.06892189292759344 0.3446078697812079 chr14 107349540 8350728 0.07779006784751942 0.4550590593935028 chr15 102531392 7245672 0.07066783995286048 0.3497293519644081 chr16 90354753 6379597 0.07060610303477892 0.4528571951035618 chr17 81195210 5672135 0.06985800024410307 0.36161903039595966 chr18 78077248 7151305 0.09159268779555345 1.2960107828412104 chr19 59128983 4880470 0.0825393868181362 0.7810913495527207 chr20 63025520 4224760 0.06703252904537717 0.36825882783962055 chr21 48129895 5362953 0.11142665073339553 0.5440338652338739 chr22 51304566 2301124 0.044852226213160054 0.2744782318269153 chrMT 16571 46377 2.798684448735743 2.403445195230988 chrX 155270560 8580838 0.055263779560014464 0.34222205930314276 chrY 59373566 633538 0.010670371390527563 0.21282288581364542