BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506024.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,408,259 number of mapped reads = 5,031,218 (78.51%) number of supplementary alignments = 197 (0%) number of secondary alignments = 0 number of mapped bases = 235,039,814 bp number of sequenced bases = 234,992,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,109 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8924 >>>>>>> ACTG content number of A's = 69,810,231 bp (29.71%) number of C's = 48,120,301 bp (20.48%) number of T's = 67,911,831 bp (28.9%) number of G's = 48,377,450 bp (20.59%) number of N's = 772,355 bp (0.33%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,814,442 number of insertions = 9,605 mapped reads with insertion percentage = 0.19% number of deletions = 34,317 mapped reads with deletion percentage = 0.68% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.0759X std coverageData = 0.629X There is a 5.71% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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% 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 23134656 0.09281684397488422 1.356935770358023 chr2 243199373 14571549 0.05991606318820567 0.4883307009987669 chr3 198022430 14301341 0.07222081357147268 0.3475584676722587 chr4 191154276 9630663 0.05038162473540482 0.29590584251314084 chr5 180915260 16787983 0.09279473163292029 0.38870739734923504 chr6 171115067 15696682 0.09173173511365892 0.456437299081144 chr7 159138663 15164315 0.09528994848976455 0.8043586448459281 chr8 146364022 13961753 0.09539060767269705 0.7856195555625872 chr9 141213431 11177589 0.07915386603700607 0.496048942380657 chr10 135534747 7350814 0.054235641875658644 0.7664466445029711 chr11 135006516 12137463 0.08990279402514172 0.5090157954902357 chr12 133851895 6335754 0.04733406277139371 0.29765543317603127 chr13 115169878 7393074 0.06419277443360667 0.31524460914809344 chr14 107349540 8414783 0.07838676346447315 0.6192824546428197 chr15 102531392 7901964 0.07706872837540331 0.3467582728613611 chr16 90354753 7648419 0.08464877326375957 0.4282679360429681 chr17 81195210 3747054 0.04614870754075271 0.3074545602827582 chr18 78077248 7548797 0.09668369715080122 0.7768153273229498 chr19 59128983 5400490 0.09133405862908212 1.0096608188310912 chr20 63025520 5138674 0.08153322654061403 0.3638128080827275 chr21 48129895 3360663 0.06982485625617924 0.3671622052996595 chr22 51304566 1484657 0.02893810660049244 0.2185391009891263 chrMT 16571 6310 0.38078570997525796 0.717600407737292 chrX 155270560 16035939 0.10327739527699263 0.4565917975840121 chrY 59373566 708428 0.011931707116934833 0.1979505052330805