BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081205.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 = 8,222,788 number of mapped reads = 6,506,789 (79.13%) number of supplementary alignments = 58,196 (0.71%) number of secondary alignments = 0 number of mapped bases = 422,360,752 bp number of sequenced bases = 422,234,503 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 863,500 duplication rate = 8.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2626 >>>>>>> ACTG content number of A's = 118,411,583 bp (28.04%) number of C's = 84,994,667 bp (20.13%) number of T's = 124,936,552 bp (29.59%) number of G's = 93,647,230 bp (22.18%) number of N's = 244,471 bp (0.06%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 4,394,753 number of insertions = 30,355 mapped reads with insertion percentage = 0.46% number of deletions = 80,513 mapped reads with deletion percentage = 1.22% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.1364X std coverageData = 1.4439X There is a 7.02% of reference with a coverageData >= 1X There is a 3.21% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 33861450 0.13585302160591206 3.2069853960840384 chr2 243199373 35652681 0.14659857285076142 1.1936430982660435 chr3 198022430 28117764 0.1419928237422397 0.6338809746699718 chr4 191154276 27275657 0.14268923285817578 0.7425844697841315 chr5 180915260 25454251 0.1406970921082058 0.6396563931157138 chr6 171115067 24611728 0.1438314488109922 0.8476501832794591 chr7 159138663 23957843 0.1505469667041252 2.046961338862327 chr8 146364022 21832045 0.14916264736152168 2.255584052809039 chr9 141213431 17652311 0.12500447638015394 1.0544020030238856 chr10 135534747 20610795 0.1520701920076628 1.5320996984960713 chr11 135006516 19416955 0.14382235447065383 1.2245947273607023 chr12 133851895 18598687 0.1389497474055186 0.6609701952192918 chr13 115169878 13373855 0.116122854623498 0.5618757246167485 chr14 107349540 12662104 0.11795210300854572 0.7825050540906506 chr15 102531392 11975732 0.1168006379938741 0.5659038327979071 chr16 90354753 11817565 0.13079073991824205 0.7077522363773144 chr17 81195210 10851176 0.13364305603741897 0.8191403880483825 chr18 78077248 11504346 0.1473456902579353 2.068129103397119 chr19 59128983 8100871 0.13700338800009465 2.108413608978588 chr20 63025520 8732540 0.13855562000916455 0.6672897298830736 chr21 48129895 5709821 0.11863356444056236 0.7063401686345702 chr22 51304566 4731746 0.09222855525178793 0.5111730476721018 chrMT 16571 162816 9.825357552350491 7.368112380281842 chrX 155270560 24422054 0.15728708648954445 0.7940272322051176 chrY 59373566 1273959 0.021456669791401782 0.5228855092580779