BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090209.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 22,193,177 number of mapped reads = 18,485,673 (83.29%) number of supplementary alignments = 1,083 (0%) number of secondary alignments = 0 number of mapped bases = 868,060,827 bp number of sequenced bases = 867,890,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,713,442 duplication rate = 10.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2438 >>>>>>> ACTG content number of A's = 271,812,125 bp (31.32%) number of C's = 170,768,820 bp (19.68%) number of T's = 242,330,179 bp (27.92%) number of G's = 182,948,202 bp (21.08%) number of N's = 30,966 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 3,212,202 number of insertions = 34,987 mapped reads with insertion percentage = 0.19% number of deletions = 113,139 mapped reads with deletion percentage = 0.61% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.2804X std coverageData = 1.723X There is a 13.98% of reference with a coverageData >= 1X There is a 5.85% of reference with a coverageData >= 2X There is a 2.92% of reference with a coverageData >= 3X There is a 1.63% of reference with a coverageData >= 4X There is a 0.98% of reference with a coverageData >= 5X There is a 0.62% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 66280894 0.2659206774854936 2.111819735660907 chr2 243199373 92320807 0.3796095600953708 1.787840134992542 chr3 198022430 81174859 0.4099275975958885 1.3417554889312733 chr4 191154276 46478868 0.24314846087983927 0.9544545627210248 chr5 180915260 34345564 0.1898433775017099 0.8174457337864953 chr6 171115067 51529493 0.3011394256707973 1.1815196189682633 chr7 159138663 65068236 0.40887760883098534 2.5563671963046644 chr8 146364022 71286913 0.4870521595805833 4.776511685644709 chr9 141213431 27776966 0.19670201200620924 1.195893614051601 chr10 135534747 27756528 0.20479270898701718 1.11127067457663 chr11 135006516 29834231 0.2209836375601308 1.1981784191815354 chr12 133851895 32121665 0.23997915756067556 0.9453569053190077 chr13 115169878 27909210 0.24233081153389777 0.9405591778048669 chr14 107349540 32222581 0.3001650589280587 1.1001655398785277 chr15 102531392 23590639 0.2300821098771389 0.9152500179578956 chr16 90354753 17944416 0.19859958003537456 0.8606742660230187 chr17 81195210 17423765 0.21459104545699187 0.9493173135546654 chr18 78077248 33023994 0.42296565063358793 1.9940612856963515 chr19 59128983 14773589 0.2498535954863286 1.6731300608061592 chr20 63025520 21529279 0.3415962137242184 1.1782968396749496 chr21 48129895 13224919 0.2747755630881804 1.1309305439103776 chr22 51304566 7229487 0.14091313042195894 0.684068811285711 chrMT 16571 194529 11.739122563514574 10.408779939206584 chrX 155270560 30905867 0.19904524721234984 0.9734406049106176 chrY 59373566 2113528 0.03559712077930438 1.0347454437863588