BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,250,958 number of mapped reads = 643,257 (51.42%) number of supplementary alignments = 3,471 (0.28%) number of secondary alignments = 0 number of mapped bases = 37,113,346 bp number of sequenced bases = 37,096,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,318 duplication rate = 5.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2058 >>>>>>> ACTG content number of A's = 10,530,639 bp (28.39%) number of C's = 6,895,474 bp (18.59%) number of T's = 11,332,535 bp (30.55%) number of G's = 8,336,015 bp (22.47%) number of N's = 1,946 bp (0.01%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 289,560 number of insertions = 2,797 mapped reads with insertion percentage = 0.43% number of deletions = 10,897 mapped reads with deletion percentage = 1.68% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.1464X There is a 0.97% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 2995833 0.012019360224582951 0.17369153920691904 chr2 243199373 3060661 0.012584987215407007 0.18230385605701918 chr3 198022430 2771690 0.013996848740821936 0.1426251223269562 chr4 191154276 2323103 0.012153026595125708 0.13391570404845277 chr5 180915260 2365093 0.01307293259838888 0.1380620993674436 chr6 171115067 2263417 0.01322745588499229 0.1489917476828538 chr7 159138663 1869450 0.011747302413870349 0.15487250768137703 chr8 146364022 2016717 0.013778775497164187 0.17173443490418783 chr9 141213431 1382200 0.009788020800939254 0.12770909355231466 chr10 135534747 1786785 0.013183224520277446 0.1517695426147967 chr11 135006516 1666775 0.012345885586737161 0.1413909734913065 chr12 133851895 1662538 0.01242072814882449 0.1355933838763216 chr13 115169878 1353710 0.011754028253811296 0.1308331233828806 chr14 107349540 949103 0.008841239561902175 0.11749737111300784 chr15 102531392 1033273 0.010077625787037008 0.12154369989436108 chr16 90354753 888068 0.009828680512247098 0.11939064258547348 chr17 81195210 903920 0.011132676422660893 0.12719700246771384 chr18 78077248 1114715 0.014277078515882117 0.17404188595536865 chr19 59128983 575880 0.009739386182238243 0.14238612427015157 chr20 63025520 889502 0.014113362333226286 0.14278096869741808 chr21 48129895 507598 0.010546418187698104 0.12444478599317597 chr22 51304566 404651 0.007887231713450222 0.10429325960441072 chrMT 16571 31076 1.875324361836944 1.9016487415286862 chrX 155270560 2196910 0.014148915286967472 0.14630131858526527 chrY 59373566 100678 0.001695670426802392 0.049046997067305156