BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618572.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 70,723,199 number of mapped reads = 68,588,141 (96.98%) number of supplementary alignments = 84,375 (0.12%) number of secondary alignments = 0 number of mapped bases = 6,720,979,077 bp number of sequenced bases = 6,716,956,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,524,472 duplication rate = 32.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.8936 >>>>>>> ACTG content number of A's = 1,768,653,428 bp (26.33%) number of C's = 1,586,298,470 bp (23.62%) number of T's = 1,788,295,223 bp (26.62%) number of G's = 1,571,699,768 bp (23.4%) number of N's = 2,009,272 bp (0.03%) GC percentage = 47.02% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 57,029,902 number of insertions = 1,034,003 mapped reads with insertion percentage = 1.48% number of deletions = 2,781,270 mapped reads with deletion percentage = 3.97% homopolymer indels = 52.98% >>>>>>> Coverage mean coverageData = 2.1711X std coverageData = 20.082X There is a 23.34% of reference with a coverageData >= 1X There is a 17.02% of reference with a coverageData >= 2X There is a 13.54% of reference with a coverageData >= 3X There is a 11.22% of reference with a coverageData >= 4X There is a 9.54% of reference with a coverageData >= 5X There is a 8.27% of reference with a coverageData >= 6X There is a 7.26% of reference with a coverageData >= 7X There is a 6.46% of reference with a coverageData >= 8X There is a 5.79% of reference with a coverageData >= 9X There is a 5.23% of reference with a coverageData >= 10X There is a 4.76% of reference with a coverageData >= 11X There is a 4.35% of reference with a coverageData >= 12X There is a 4% of reference with a coverageData >= 13X There is a 3.69% of reference with a coverageData >= 14X There is a 3.42% of reference with a coverageData >= 15X There is a 3.18% of reference with a coverageData >= 16X There is a 2.97% of reference with a coverageData >= 17X There is a 2.77% of reference with a coverageData >= 18X There is a 2.6% of reference with a coverageData >= 19X There is a 2.44% of reference with a coverageData >= 20X There is a 2.3% of reference with a coverageData >= 21X There is a 2.17% of reference with a coverageData >= 22X There is a 2.05% of reference with a coverageData >= 23X There is a 1.94% of reference with a coverageData >= 24X There is a 1.84% of reference with a coverageData >= 25X There is a 1.74% of reference with a coverageData >= 26X There is a 1.66% of reference with a coverageData >= 27X There is a 1.58% of reference with a coverageData >= 28X There is a 1.5% of reference with a coverageData >= 29X There is a 1.43% of reference with a coverageData >= 30X There is a 1.37% of reference with a coverageData >= 31X There is a 1.31% of reference with a coverageData >= 32X There is a 1.25% of reference with a coverageData >= 33X There is a 1.2% of reference with a coverageData >= 34X There is a 1.15% of reference with a coverageData >= 35X There is a 1.1% of reference with a coverageData >= 36X There is a 1.06% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.94% of reference with a coverageData >= 40X There is a 0.9% of reference with a coverageData >= 41X There is a 0.87% of reference with a coverageData >= 42X There is a 0.84% of reference with a coverageData >= 43X There is a 0.81% of reference with a coverageData >= 44X There is a 0.78% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.73% of reference with a coverageData >= 47X There is a 0.7% of reference with a coverageData >= 48X There is a 0.68% of reference with a coverageData >= 49X There is a 0.66% of reference with a coverageData >= 50X There is a 0.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 636778068 2.554770236660714 19.73290632138283 chr2 243199373 563720981 2.317937641229034 19.455264710325732 chr3 198022430 420779158 2.124906547202759 21.613259238746533 chr4 191154276 296503668 1.5511223405747931 21.43294578618746 chr5 180915260 370281517 2.0467124608504554 33.32779617247983 chr6 171115067 336203320 1.9647791740045895 16.302244245991524 chr7 159138663 340004737 2.1365313154604046 18.878848810193574 chr8 146364022 324133350 2.2145698483196914 22.7602616600006 chr9 141213431 305546473 2.1637210486019565 16.45423051560303 chr10 135534747 361005943 2.663567468790863 19.478339333309783 chr11 135006516 358709204 2.6569769713929956 18.928584619937666 chr12 133851895 321274554 2.40022417314301 20.059469403656404 chr13 115169878 164446908 1.4278638725309756 14.356766470129338 chr14 107349540 216998939 2.0214240228695903 14.360576015127007 chr15 102531392 241762469 2.357936084589586 20.808217452164318 chr16 90354753 272737181 3.018515041483208 24.009454933695682 chr17 81195210 281224026 3.4635543894769163 21.08774932336926 chr18 78077248 170341181 2.181700628075416 17.535995314445483 chr19 59128983 198967557 3.364975125650309 16.745737133061283 chr20 63025520 216631679 3.437205738246983 15.628838778318618 chr21 48129895 91564558 1.9024466602306114 16.27920084009906 chr22 51304566 166554944 3.2463961199866693 31.511809441757567 chrMT 16571 13803 0.8329611972723433 3.195797455782507 chrX 155270560 11541340 0.07433051056169308 3.587196978184562 chrY 59373566 53253519 0.8969230347390622 10.49061385256917