BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163148.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 = 97,880,114 number of mapped reads = 96,570,149 (98.66%) number of supplementary alignments = 403,145 (0.41%) number of secondary alignments = 0 number of mapped bases = 9,166,543,161 bp number of sequenced bases = 9,165,470,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,272,264 duplication rate = 48.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1131 >>>>>>> ACTG content number of A's = 2,233,944,647 bp (24.37%) number of C's = 2,349,720,646 bp (25.64%) number of T's = 2,217,438,551 bp (24.19%) number of G's = 2,364,008,235 bp (25.79%) number of N's = 358,413 bp (0%) GC percentage = 51.43% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 33,711,616 number of insertions = 584,855 mapped reads with insertion percentage = 0.6% number of deletions = 488,263 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 2.9611X std coverageData = 37.5035X There is a 8.93% of reference with a coverageData >= 1X There is a 6.13% of reference with a coverageData >= 2X There is a 4.64% of reference with a coverageData >= 3X There is a 4.16% of reference with a coverageData >= 4X There is a 3.78% of reference with a coverageData >= 5X There is a 3.54% of reference with a coverageData >= 6X There is a 3.35% of reference with a coverageData >= 7X There is a 3.19% of reference with a coverageData >= 8X There is a 3.06% of reference with a coverageData >= 9X There is a 2.94% of reference with a coverageData >= 10X There is a 2.84% of reference with a coverageData >= 11X There is a 2.74% of reference with a coverageData >= 12X There is a 2.66% of reference with a coverageData >= 13X There is a 2.58% of reference with a coverageData >= 14X There is a 2.51% of reference with a coverageData >= 15X There is a 2.44% of reference with a coverageData >= 16X There is a 2.37% of reference with a coverageData >= 17X There is a 2.32% of reference with a coverageData >= 18X There is a 2.26% of reference with a coverageData >= 19X There is a 2.21% of reference with a coverageData >= 20X There is a 2.16% of reference with a coverageData >= 21X There is a 2.11% of reference with a coverageData >= 22X There is a 2.06% of reference with a coverageData >= 23X There is a 2.02% of reference with a coverageData >= 24X There is a 1.98% of reference with a coverageData >= 25X There is a 1.94% of reference with a coverageData >= 26X There is a 1.9% of reference with a coverageData >= 27X There is a 1.86% of reference with a coverageData >= 28X There is a 1.83% of reference with a coverageData >= 29X There is a 1.79% of reference with a coverageData >= 30X There is a 1.76% of reference with a coverageData >= 31X There is a 1.73% of reference with a coverageData >= 32X There is a 1.7% of reference with a coverageData >= 33X There is a 1.67% of reference with a coverageData >= 34X There is a 1.64% of reference with a coverageData >= 35X There is a 1.62% of reference with a coverageData >= 36X There is a 1.59% of reference with a coverageData >= 37X There is a 1.56% of reference with a coverageData >= 38X There is a 1.54% of reference with a coverageData >= 39X There is a 1.51% of reference with a coverageData >= 40X There is a 1.49% of reference with a coverageData >= 41X There is a 1.47% of reference with a coverageData >= 42X There is a 1.44% of reference with a coverageData >= 43X There is a 1.42% of reference with a coverageData >= 44X There is a 1.4% of reference with a coverageData >= 45X There is a 1.38% of reference with a coverageData >= 46X There is a 1.36% of reference with a coverageData >= 47X There is a 1.34% of reference with a coverageData >= 48X There is a 1.32% of reference with a coverageData >= 49X There is a 1.3% of reference with a coverageData >= 50X There is a 1.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1371140871 5.50105297831936 52.314988383441204 chr2 243199373 401568495 1.651190502863673 19.85485236071775 chr3 198022430 369919335 1.868067849687533 20.711634874048915 chr4 191154276 189210450 0.9898311142147822 16.41875040647538 chr5 180915260 513695830 2.839427862525251 49.38284523225628 chr6 171115067 537269085 3.139811674211015 37.11576916905445 chr7 159138663 559453071 3.5155069198991575 42.37151337655331 chr8 146364022 441223297 3.014561167224552 54.020022776444186 chr9 141213431 457653527 3.2408640152649504 35.16011198636641 chr10 135534747 217932452 1.6079452452144984 25.309821661991464 chr11 135006516 484529706 3.5889357073698576 32.851465997793 chr12 133851895 252164435 1.8839063503732987 20.40353885023893 chr13 115169878 125657000 1.0910578545546432 16.97413678879189 chr14 107349540 248245860 2.3125004541239766 23.829996509179246 chr15 102531392 440706815 4.298262282443215 41.81689082284665 chr16 90354753 392501776 4.344008067843426 38.601580149973856 chr17 81195210 267761742 3.2977529339477045 27.27509862949884 chr18 78077248 157461491 2.016739767774602 25.447398951222183 chr19 59128983 739480188 12.506221999454988 95.87838010933582 chr20 63025520 229891014 3.6475861524030266 36.93948216111902 chr21 48129895 131691712 2.7361728505744716 57.66369453238081 chr22 51304566 117395215 2.288202087120277 29.017689295011717 chrMT 16571 544 0.032828435218152194 0.23435814932373492 chrX 155270560 513624250 3.307930685636736 37.87302749651954 chrY 59373566 6365000 0.1072025891117943 6.028296711930174