BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084867.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 = 2,705,038 number of mapped reads = 2,421,321 (89.51%) number of supplementary alignments = 18,403 (0.68%) number of secondary alignments = 0 number of mapped bases = 168,239,422 bp number of sequenced bases = 168,174,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,697 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6847 >>>>>>> ACTG content number of A's = 49,350,000 bp (29.34%) number of C's = 30,765,382 bp (18.29%) number of T's = 53,969,701 bp (32.09%) number of G's = 34,063,387 bp (20.25%) number of N's = 26,284 bp (0.02%) GC percentage = 38.55% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,386,869 number of insertions = 13,242 mapped reads with insertion percentage = 0.54% number of deletions = 36,394 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.4108X There is a 4.52% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 13036334 0.05230211241880918 0.6434349799532447 chr2 243199373 13518322 0.05558534889808289 0.42988623562757555 chr3 198022430 14290663 0.07216689038711423 0.30971290553075814 chr4 191154276 10221488 0.05347245279514438 0.268686217250612 chr5 180915260 8696534 0.04806965426797054 0.25745127914994326 chr6 171115067 9970829 0.05826973144334508 0.28640486322993186 chr7 159138663 11252630 0.0707095924263232 0.45324462012317346 chr8 146364022 9872748 0.06745338003898253 0.880102483007391 chr9 141213431 13152689 0.09314049596316373 0.4677495462205877 chr10 135534747 5156103 0.038042665177218354 0.2963924676904109 chr11 135006516 7017156 0.05197642460457242 0.3426567296301949 chr12 133851895 6888387 0.051462752918066644 0.2631711850233914 chr13 115169878 5000520 0.043418644586911866 0.23739697691081202 chr14 107349540 3239616 0.030178201043059894 0.21130994622967963 chr15 102531392 3944198 0.03846819908579804 0.22380070793676257 chr16 90354753 2856731 0.031616831490868004 0.22837903463644152 chr17 81195210 3690256 0.04544918351710649 0.253524934924615 chr18 78077248 7229576 0.09259516933793568 0.6908363638895318 chr19 59128983 2740654 0.04635043359362362 0.41480842220403047 chr20 63025520 2885079 0.045776361702370726 0.25002016986037806 chr21 48129895 1502511 0.031217832492674253 0.21707330588290927 chr22 51304566 1319633 0.025721550787506906 0.1795045296889443 chrMT 16571 66169 3.993060165349104 2.777923726566916 chrX 155270560 10309372 0.06639617967501373 0.31993522532368956 chrY 59373566 381224 0.00642076980857104 0.2063135362170396