BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153312.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 = 223,286,584 number of mapped reads = 218,198,999 (97.72%) number of supplementary alignments = 1,333,368 (0.6%) number of secondary alignments = 0 number of mapped bases = 21,436,161,934 bp number of sequenced bases = 21,432,771,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,360,465 duplication rate = 38.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3242 >>>>>>> ACTG content number of A's = 5,385,427,324 bp (25.13%) number of C's = 5,328,716,462 bp (24.86%) number of T's = 5,434,525,587 bp (25.36%) number of G's = 5,280,062,955 bp (24.64%) number of N's = 4,039,118 bp (0.02%) GC percentage = 49.5% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 88,214,974 number of insertions = 1,207,989 mapped reads with insertion percentage = 0.55% number of deletions = 1,546,249 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.02% >>>>>>> Coverage mean coverageData = 6.9245X std coverageData = 56.7443X There is a 59.83% of reference with a coverageData >= 1X There is a 42.39% of reference with a coverageData >= 2X There is a 29.71% of reference with a coverageData >= 3X There is a 21.88% of reference with a coverageData >= 4X There is a 16.69% of reference with a coverageData >= 5X There is a 13.3% of reference with a coverageData >= 6X There is a 10.99% of reference with a coverageData >= 7X There is a 9.38% of reference with a coverageData >= 8X There is a 8.22% of reference with a coverageData >= 9X There is a 7.37% of reference with a coverageData >= 10X There is a 6.71% of reference with a coverageData >= 11X There is a 6.2% of reference with a coverageData >= 12X There is a 5.79% of reference with a coverageData >= 13X There is a 5.45% of reference with a coverageData >= 14X There is a 5.17% of reference with a coverageData >= 15X There is a 4.94% of reference with a coverageData >= 16X There is a 4.73% of reference with a coverageData >= 17X There is a 4.55% of reference with a coverageData >= 18X There is a 4.39% of reference with a coverageData >= 19X There is a 4.25% of reference with a coverageData >= 20X There is a 4.12% of reference with a coverageData >= 21X There is a 4% of reference with a coverageData >= 22X There is a 3.89% of reference with a coverageData >= 23X There is a 3.79% of reference with a coverageData >= 24X There is a 3.69% of reference with a coverageData >= 25X There is a 3.6% of reference with a coverageData >= 26X There is a 3.52% of reference with a coverageData >= 27X There is a 3.44% of reference with a coverageData >= 28X There is a 3.37% of reference with a coverageData >= 29X There is a 3.3% of reference with a coverageData >= 30X There is a 3.23% of reference with a coverageData >= 31X There is a 3.17% of reference with a coverageData >= 32X There is a 3.11% of reference with a coverageData >= 33X There is a 3.05% of reference with a coverageData >= 34X There is a 3% of reference with a coverageData >= 35X There is a 2.94% of reference with a coverageData >= 36X There is a 2.89% of reference with a coverageData >= 37X There is a 2.84% of reference with a coverageData >= 38X There is a 2.79% of reference with a coverageData >= 39X There is a 2.75% of reference with a coverageData >= 40X There is a 2.7% of reference with a coverageData >= 41X There is a 2.66% of reference with a coverageData >= 42X There is a 2.62% of reference with a coverageData >= 43X There is a 2.58% of reference with a coverageData >= 44X There is a 2.54% of reference with a coverageData >= 45X There is a 2.5% of reference with a coverageData >= 46X There is a 2.46% of reference with a coverageData >= 47X There is a 2.43% of reference with a coverageData >= 48X There is a 2.39% of reference with a coverageData >= 49X There is a 2.36% of reference with a coverageData >= 50X There is a 2.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2079684096 8.34374689882919 55.10761243438619 chr2 243199373 1183662508 4.867045886668466 28.135651631406027 chr3 198022430 1037406957 5.23883560564326 30.44483828989102 chr4 191154276 615936070 3.2221935228903797 29.18241029820488 chr5 180915260 1288117545 7.120004940434543 108.41010782123767 chr6 171115067 572487900 3.345631159411579 22.2862319440281 chr7 159138663 1139268659 7.158968396008203 79.22327522912758 chr8 146364022 1236025076 8.444869573207 96.70187048776575 chr9 141213431 556965599 3.944140405454776 23.97168980104494 chr10 135534747 1015070164 7.48937218291336 40.95975216456453 chr11 135006516 1032375119 7.646854015549886 40.06262326571008 chr12 133851895 935427501 6.988526393294618 36.06326992012929 chr13 115169878 201319993 1.7480264501105054 11.06169912187263 chr14 107349540 534888580 4.9826816211788145 28.200013816394897 chr15 102531392 1063529961 10.372725272275636 58.50084396060145 chr16 90354753 1285967282 14.23242540433927 85.9281928794625 chr17 81195210 1243676820 15.317120554279002 91.54042701962713 chr18 78077248 193481388 2.478076430152866 16.57469384923846 chr19 59128983 1625292549 27.48724003928835 106.47517918178102 chr20 63025520 661815273 10.500750695908579 50.985290271494314 chr21 48129895 275186324 5.717575822677361 61.40231026956942 chr22 51304566 566087962 11.033870981385945 68.27124180981278 chrMT 16571 72048 4.347836581980569 2.9809798398073273 chrX 155270560 1066867044 6.871019490108106 39.65744850317334 chrY 59373566 25549516 0.4303180307546291 18.83412079711845