BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081142.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 = 2,670,478 number of mapped reads = 2,369,005 (88.71%) number of supplementary alignments = 22,808 (0.85%) number of secondary alignments = 0 number of mapped bases = 157,772,496 bp number of sequenced bases = 157,715,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,952 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6905 >>>>>>> ACTG content number of A's = 44,936,657 bp (28.49%) number of C's = 29,410,160 bp (18.65%) number of T's = 49,141,906 bp (31.16%) number of G's = 34,180,269 bp (21.67%) number of N's = 46,476 bp (0.03%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,321,325 number of insertions = 12,010 mapped reads with insertion percentage = 0.5% number of deletions = 35,277 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.3936X There is a 4.28% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% 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% 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 11607238 0.04656854194959057 0.6099568310542933 chr2 243199373 13710010 0.05637354171961619 0.46928259041872494 chr3 198022430 10905082 0.055069933239381016 0.2685480798574389 chr4 191154276 10331170 0.054046240639681005 0.2779655010637131 chr5 180915260 10765161 0.0595038859629641 0.2817751005302884 chr6 171115067 9871017 0.057686428045520974 0.3660573037704242 chr7 159138663 8832432 0.05550148426218712 0.5405926935608566 chr8 146364022 8534758 0.05831185754105609 0.5775628320556424 chr9 141213431 6002337 0.042505425705576125 0.34957843621120366 chr10 135534747 6802888 0.05019294424919685 0.3508648296534539 chr11 135006516 7132706 0.052832309219800914 0.3721246586120242 chr12 133851895 7413535 0.05538610417133056 0.2746238551677255 chr13 115169878 4825835 0.041901885143960996 0.23517772865583242 chr14 107349540 4804416 0.04475488204234503 0.2666334407845672 chr15 102531392 4437219 0.043276687397358266 0.2406679707392446 chr16 90354753 4630195 0.05124462019170148 0.2851173976810185 chr17 81195210 3291750 0.04054118463392114 0.2494625469834938 chr18 78077248 4541376 0.05816516483777707 0.6860754479030416 chr19 59128983 1985551 0.03357999578649949 0.46057793767183874 chr20 63025520 2661662 0.042231496066990004 0.24581176319652717 chr21 48129895 2221504 0.04615642730988713 0.2627819776546074 chr22 51304566 1664460 0.03244272644271077 0.20439609170592363 chrMT 16571 31302 1.8889626455856616 1.6929954845411619 chrX 155270560 10367720 0.06677196243769586 0.32494681755403293 chrY 59373566 401172 0.006756744238673487 0.13532913171003216