BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080756.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 = 10,004,039 number of mapped reads = 7,963,109 (79.6%) number of supplementary alignments = 34,094 (0.34%) number of secondary alignments = 0 number of mapped bases = 510,814,833 bp number of sequenced bases = 510,654,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,231,026 duplication rate = 11.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9736 >>>>>>> ACTG content number of A's = 158,280,559 bp (31%) number of C's = 102,695,263 bp (20.11%) number of T's = 131,346,674 bp (25.72%) number of G's = 117,155,860 bp (22.94%) number of N's = 1,175,874 bp (0.23%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 5,168,247 number of insertions = 36,006 mapped reads with insertion percentage = 0.45% number of deletions = 85,354 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.44% >>>>>>> Coverage mean coverageData = 0.165X std coverageData = 0.9506X There is a 8.93% of reference with a coverageData >= 1X There is a 3.52% of reference with a coverageData >= 2X There is a 1.65% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 60543444 0.24290187826653398 1.3413718278378914 chr2 243199373 35526982 0.14608171707745315 0.8822049262865873 chr3 198022430 30435481 0.15369713925841633 0.6679762928755685 chr4 191154276 27470889 0.1437105649679529 0.8362457945204768 chr5 180915260 36029168 0.19914941393003552 0.7667826708335546 chr6 171115067 35274899 0.20614724125959055 1.0542820507359212 chr7 159138663 36589309 0.22992092751212823 1.5315980184196554 chr8 146364022 20383110 0.13926311754400955 1.1657058331026742 chr9 141213431 17618591 0.12476568889541392 0.7030823648928021 chr10 135534747 19184330 0.1415454739440359 1.083673212855567 chr11 135006516 22788679 0.16879688236677406 0.9130575014473177 chr12 133851895 19241015 0.14374854386633823 0.6748310692412453 chr13 115169878 27823337 0.2415851912250875 0.8827602068352071 chr14 107349540 14113596 0.1314732787862901 0.6799381317989855 chr15 102531392 12852727 0.125354067171935 0.6178589899353972 chr16 90354753 13747137 0.15214625178600177 0.7963848140718384 chr17 81195210 15174649 0.18689093851718594 0.8314942385337455 chr18 78077248 7272578 0.09314593157791627 1.0103503690227094 chr19 59128983 9253012 0.1564886039051272 1.1570577416225856 chr20 63025520 9310778 0.14773028449428105 0.7169290830907303 chr21 48129895 7717140 0.1603398469911476 0.9259773414576477 chr22 51304566 3268991 0.06371735022570896 0.4297604191461896 chrMT 16571 102009 6.1558747208979545 5.416423642783273 chrX 155270560 27570634 0.17756510957389476 0.7600634717277635 chrY 59373566 1522348 0.02564016451361537 0.7696529879486664