BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818841.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,495,181 number of mapped reads = 2,431,855 (97.46%) number of supplementary alignments = 35,723 (1.43%) number of secondary alignments = 0 number of mapped bases = 225,500,140 bp number of sequenced bases = 225,364,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 623,494 duplication rate = 22.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3528 >>>>>>> ACTG content number of A's = 64,202,658 bp (28.49%) number of C's = 47,067,181 bp (20.88%) number of T's = 65,455,857 bp (29.04%) number of G's = 48,636,033 bp (21.58%) number of N's = 3,116 bp (0%) GC percentage = 42.47% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,323,063 number of insertions = 31,319 mapped reads with insertion percentage = 1.24% number of deletions = 71,424 mapped reads with deletion percentage = 2.87% homopolymer indels = 40.96% >>>>>>> Coverage mean coverageData = 0.0728X std coverageData = 0.8077X There is a 4.69% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 20723775 0.08314432644883962 1.2576855205848654 chr2 243199373 16367691 0.06730153453150556 1.1462714721037879 chr3 198022430 13503873 0.06819365361792601 0.3718908781316333 chr4 191154276 13118495 0.06862778732713257 0.45670161794481073 chr5 180915260 11448962 0.06328356159673872 0.38363095054028556 chr6 171115067 10836758 0.06333023847631138 0.4064846620895578 chr7 159138663 19014050 0.11948102140332799 1.718541599317069 chr8 146364022 21745249 0.14856963277491786 0.7243186031828586 chr9 141213431 8071220 0.05715617801255746 0.690453444500608 chr10 135534747 9830418 0.07253061091411489 0.9609505975022297 chr11 135006516 9340809 0.06918783831144862 0.487883580845022 chr12 133851895 8524721 0.06368771245263281 0.36409875735083513 chr13 115169878 5384110 0.04674928977523098 0.3020531413005959 chr14 107349540 7423370 0.06915139086762738 0.4295670715521638 chr15 102531392 6075231 0.0592523994992675 0.3626110758651099 chr16 90354753 5290501 0.058552547866518985 0.8340984930446362 chr17 81195210 5958708 0.07338743258376941 0.5212127836396162 chr18 78077248 3733714 0.04782076847790537 0.7616889576602348 chr19 59128983 4119783 0.06967451139824272 1.1077750162948583 chr20 63025520 8892859 0.14109933563420024 0.5874114188440505 chr21 48129895 2046224 0.04251461591594995 0.3419980105680109 chr22 51304566 2636374 0.05138673232320102 0.3713875315686682 chrMT 16571 596082 35.971395811960654 21.431137695457327 chrX 155270560 10066483 0.06483188442161862 0.4574671851136497 chrY 59373566 750680 0.012643336935497525 0.9185729434061964