BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549075.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,084,090 number of mapped reads = 8,790,989 (87.18%) number of secondary alignments = 0 number of mapped bases = 347,983,694 bp number of sequenced bases = 347,950,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,473 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3749 >>>>>>> ACTG content number of A's = 105,003,568 bp (30.18%) number of C's = 68,703,321 bp (19.75%) number of T's = 106,621,113 bp (30.64%) number of G's = 67,535,277 bp (19.41%) number of N's = 86,892 bp (0.02%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 1,522,206 number of insertions = 10,442 mapped reads with insertion percentage = 0.12% number of deletions = 27,356 mapped reads with deletion percentage = 0.31% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.1124X std coverageData = 1.4096X There is a 9.59% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 0.01% 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 27752360 0.11134319300251613 3.8502670823155642 chr2 243199373 31069682 0.12775395601040468 0.929827641923606 chr3 198022430 24837627 0.12542835172763003 0.4316973970628602 chr4 191154276 24915471 0.13034221112584476 0.4237860954866177 chr5 180915260 22970720 0.1269694994219946 0.4404045223936423 chr6 171115067 21396443 0.12504125659489704 0.6337181427227093 chr7 159138663 19524350 0.12268765887520369 1.399808792894097 chr8 146364022 19082058 0.13037396580971244 0.7361415938758481 chr9 141213431 14806013 0.10484847577989943 0.9519680420644736 chr10 135534747 16626432 0.12267283754180026 1.2657463128300788 chr11 135006516 15784277 0.11691492727654716 0.9288044105475576 chr12 133851895 16033965 0.11978885319479414 0.4925175893873126 chr13 115169878 12165766 0.10563322816057859 0.35109207224790284 chr14 107349540 10715581 0.09981953346050668 0.7447801392320185 chr15 102531392 9370918 0.09139559911563475 0.342583786619588 chr16 90354753 8863084 0.09809206163177714 0.653533655507619 chr17 81195210 7516005 0.09256709847785356 0.5020301499044096 chr18 78077248 10147327 0.12996522367181795 2.2108411454167562 chr19 59128983 5529686 0.09351904462824939 3.0864729586327955 chr20 63025520 6468957 0.10264027968353137 0.42260580497673844 chr21 48129895 4477929 0.09303841198905587 0.49982666182328517 chr22 51304566 2809956 0.05477009590140573 0.36616675323297265 chrMT 16571 14394 0.8686259127391226 1.3398673892761321 chrX 155270560 12460743 0.08025180691046647 0.6123327447332964 chrY 59373566 2643950 0.044530759698684766 0.33247178445311587