BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013278.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 = 3,401,280 number of mapped reads = 3,085,750 (90.72%) number of supplementary alignments = 31,011 (0.91%) number of secondary alignments = 0 number of mapped bases = 201,257,199 bp number of sequenced bases = 201,175,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,720 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.081 >>>>>>> ACTG content number of A's = 56,064,070 bp (27.87%) number of C's = 39,074,594 bp (19.42%) number of T's = 60,210,894 bp (29.93%) number of G's = 45,782,891 bp (22.76%) number of N's = 43,364 bp (0.02%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,644,135 number of insertions = 14,534 mapped reads with insertion percentage = 0.47% number of deletions = 47,298 mapped reads with deletion percentage = 1.52% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.065X std coverageData = 0.6062X There is a 5.66% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 13474489 0.054060001720116074 1.0637545229828878 chr2 243199373 23554317 0.09685188209757432 0.6970236606283455 chr3 198022430 11866541 0.059925236752220445 0.2712213961929689 chr4 191154276 12032160 0.06294475986506314 0.2915552905180718 chr5 180915260 10019917 0.05538458723714075 0.26399187952579095 chr6 171115067 10895854 0.06367559672579855 0.4515113552248357 chr7 159138663 12516928 0.0786542237067808 1.35551178762607 chr8 146364022 11495198 0.07853841294413186 0.48925554458272175 chr9 141213431 6718445 0.047576529742415226 0.476323897488568 chr10 135534747 10031807 0.07401649556331115 0.6796117565579972 chr11 135006516 8050835 0.05963293653174488 0.4328236413432816 chr12 133851895 11048584 0.08254335136607517 0.32629775318017956 chr13 115169878 4192926 0.03640644648421005 0.2141808223439246 chr14 107349540 6660740 0.06204721510683697 0.3338753614242656 chr15 102531392 5920189 0.05774025773491888 0.26748994150169814 chr16 90354753 7266385 0.08042061716443406 0.35462561835904616 chr17 81195210 4783269 0.058910728847181994 0.34695680530049566 chr18 78077248 4443865 0.05691626067558119 0.9128931482703445 chr19 59128983 3790658 0.06410829017640976 0.8123608216157115 chr20 63025520 4610815 0.07315790492486218 0.31118059389967717 chr21 48129895 3657824 0.07599900228330023 0.33626444034317626 chr22 51304566 1706994 0.03327177545951758 0.19753855383469907 chrMT 16571 361177 21.795727475710578 14.438961911293914 chrX 155270560 11705286 0.07538638361322327 0.3665927873778654 chrY 59373566 451996 0.007612748070412345 0.13603768718679432