BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153327.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 = 60,998,036 number of mapped reads = 60,516,961 (99.21%) number of supplementary alignments = 323,866 (0.53%) number of secondary alignments = 0 number of mapped bases = 5,890,980,232 bp number of sequenced bases = 5,890,230,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,633,512 duplication rate = 61.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.53 >>>>>>> ACTG content number of A's = 1,557,247,350 bp (26.44%) number of C's = 1,378,099,319 bp (23.4%) number of T's = 1,602,032,410 bp (27.2%) number of G's = 1,350,868,700 bp (22.93%) number of N's = 1,982,835 bp (0.03%) GC percentage = 46.33% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 16,082,948 number of insertions = 420,173 mapped reads with insertion percentage = 0.69% number of deletions = 371,368 mapped reads with deletion percentage = 0.61% homopolymer indels = 49.81% >>>>>>> Coverage mean coverageData = 1.903X std coverageData = 21.9623X There is a 11.36% of reference with a coverageData >= 1X There is a 8.11% of reference with a coverageData >= 2X There is a 5.56% of reference with a coverageData >= 3X There is a 4.62% of reference with a coverageData >= 4X There is a 3.65% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.89% of reference with a coverageData >= 7X There is a 2.72% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2.38% of reference with a coverageData >= 10X There is a 2.25% of reference with a coverageData >= 11X There is a 2.17% of reference with a coverageData >= 12X There is a 2.08% of reference with a coverageData >= 13X There is a 2.01% of reference with a coverageData >= 14X There is a 1.94% of reference with a coverageData >= 15X There is a 1.88% of reference with a coverageData >= 16X There is a 1.82% of reference with a coverageData >= 17X There is a 1.77% of reference with a coverageData >= 18X There is a 1.72% of reference with a coverageData >= 19X There is a 1.67% of reference with a coverageData >= 20X There is a 1.63% of reference with a coverageData >= 21X There is a 1.59% of reference with a coverageData >= 22X There is a 1.55% of reference with a coverageData >= 23X There is a 1.51% of reference with a coverageData >= 24X There is a 1.48% of reference with a coverageData >= 25X There is a 1.44% of reference with a coverageData >= 26X There is a 1.41% of reference with a coverageData >= 27X There is a 1.38% of reference with a coverageData >= 28X There is a 1.35% of reference with a coverageData >= 29X There is a 1.32% of reference with a coverageData >= 30X There is a 1.29% of reference with a coverageData >= 31X There is a 1.27% of reference with a coverageData >= 32X There is a 1.24% of reference with a coverageData >= 33X There is a 1.22% of reference with a coverageData >= 34X There is a 1.19% of reference with a coverageData >= 35X There is a 1.17% of reference with a coverageData >= 36X There is a 1.15% of reference with a coverageData >= 37X There is a 1.13% of reference with a coverageData >= 38X There is a 1.1% of reference with a coverageData >= 39X There is a 1.08% of reference with a coverageData >= 40X There is a 1.06% of reference with a coverageData >= 41X There is a 1.05% of reference with a coverageData >= 42X There is a 1.03% of reference with a coverageData >= 43X There is a 1.01% of reference with a coverageData >= 44X There is a 0.99% of reference with a coverageData >= 45X There is a 0.97% of reference with a coverageData >= 46X There is a 0.96% of reference with a coverageData >= 47X There is a 0.94% of reference with a coverageData >= 48X There is a 0.93% of reference with a coverageData >= 49X There is a 0.91% of reference with a coverageData >= 50X There is a 0.9% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 589172100 2.3637738499355634 21.969966456046006 chr2 243199373 438359865 1.802471197160529 16.74237104806205 chr3 198022430 308692541 1.558876643418627 15.048671253912785 chr4 191154276 235207398 1.2304584700998267 13.428570200932722 chr5 180915260 370400928 2.0473724991468383 20.49301055537886 chr6 171115067 211432388 1.2356152599934405 15.097905166200581 chr7 159138663 283363543 1.7806077898241486 18.730817879249948 chr8 146364022 333266252 2.2769683932298608 45.14423334427228 chr9 141213431 148926831 1.0546222830603131 10.860768624170401 chr10 135534747 289740756 2.137759964977837 20.66898097930829 chr11 135006516 280455159 2.0773453556863877 18.767199580742535 chr12 133851895 295675221 2.2089729921268577 18.659799699533185 chr13 115169878 77720408 0.6748327718120879 8.806797446173123 chr14 107349540 171680884 1.5992698617991283 15.659483987473296 chr15 102531392 291517676 2.843204118403074 29.35847388883876 chr16 90354753 273520397 3.0271832739114455 29.5286677145526 chr17 81195210 228383603 2.812771874104396 20.835400320408432 chr18 78077248 68117758 0.8724405604049978 10.304299868345423 chr19 59128983 283092829 4.787716862980715 35.833027838828 chr20 63025520 167460636 2.657029025702604 45.15387333974459 chr21 48129895 55690333 1.1570840326994272 12.82055121006582 chr22 51304566 84443516 1.64592593961325 16.44919329327323 chrMT 16571 16428 0.9913704664775813 2.791615743356252 chrX 155270560 401298596 2.584511809579356 27.02158400356178 chrY 59373566 3344186 0.05632449295701727 2.096383607811966