BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085016.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 = 3,130,667 number of mapped reads = 2,822,391 (90.15%) number of supplementary alignments = 31,526 (1.01%) number of secondary alignments = 0 number of mapped bases = 186,382,239 bp number of sequenced bases = 186,313,457 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,335 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8032 >>>>>>> ACTG content number of A's = 53,165,123 bp (28.54%) number of C's = 34,403,197 bp (18.47%) number of T's = 58,145,677 bp (31.21%) number of G's = 40,573,723 bp (21.78%) number of N's = 25,737 bp (0.01%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,592,881 number of insertions = 14,761 mapped reads with insertion percentage = 0.52% number of deletions = 42,919 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.5969X There is a 5.17% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13690052 0.05492484610499727 1.2241546935191077 chr2 243199373 16832132 0.06921124751419487 0.6699761008047392 chr3 198022430 13033964 0.06582064466131438 0.2897501902427622 chr4 191154276 12849302 0.0672195373751409 0.2992041399539192 chr5 180915260 12304099 0.0680102883526796 0.29851393112557967 chr6 171115067 10036238 0.058651982995746366 0.3823155623224652 chr7 159138663 9174766 0.057652652265904734 0.4884104739492148 chr8 146364022 8572443 0.05856933201794632 0.9585501435251698 chr9 141213431 7811697 0.055318371239064364 0.5529541203015212 chr10 135534747 8747614 0.06454148617697276 0.6246366536881763 chr11 135006516 8475438 0.0627779921378017 0.5693194475109188 chr12 133851895 9132016 0.06822477933539903 0.30975554937519384 chr13 115169878 6043806 0.05247731529245868 0.2549424955468511 chr14 107349540 5483142 0.051077461533603215 0.3141812015654799 chr15 102531392 5529344 0.053928303245897605 0.26376181281371786 chr16 90354753 5304064 0.05870265618456176 0.35862041712758774 chr17 81195210 4540748 0.05592384082755621 0.36505435678781756 chr18 78077248 5285253 0.06769261385852124 1.0821958293465423 chr19 59128983 3540946 0.05988511589993016 0.8535351972560866 chr20 63025520 3677535 0.058349935073919265 0.2886025053808792 chr21 48129895 2508781 0.0521252124069666 0.2970524011685244 chr22 51304566 1778440 0.03466436106291202 0.20672793594113978 chrMT 16571 50334 3.0374751071148394 2.481807892626228 chrX 155270560 11534103 0.07428390159731503 0.3998665356182652 chrY 59373566 445982 0.007511457203025333 0.14324216849170177