BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094040.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 406,768 number of mapped reads = 375,851 (92.4%) number of supplementary alignments = 9,259 (2.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 188,620 number of mapped paired reads (second in pair) = 187,231 number of mapped paired reads (both in pair) = 373,228 number of mapped paired reads (singletons) = 2,623 number of mapped bases = 49,338,845 bp number of sequenced bases = 47,644,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,278 duplication rate = 51.89% >>>>>>> Insert size mean insert size = 150,516.4664 std insert size = 4,217,872.8004 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 44.6737 >>>>>>> ACTG content number of A's = 13,303,407 bp (27.92%) number of C's = 10,500,923 bp (22.04%) number of T's = 13,043,292 bp (27.38%) number of G's = 10,796,036 bp (22.66%) number of N's = 432 bp (0%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0528 number of mismatches = 2,482,471 number of insertions = 32,557 mapped reads with insertion percentage = 8.49% number of deletions = 166,676 mapped reads with deletion percentage = 41.4% homopolymer indels = 31.79% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 5.6122X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% 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 2495144 0.010010582882359198 3.480144062290666 chr2 243199373 3379958 0.013897889448917289 4.24961030956022 chr3 198022430 2584728 0.013052703171049866 4.1873932975755395 chr4 191154276 2935573 0.015357087800641196 4.374904264945925 chr5 180915260 1670814 0.009235340346635215 3.8720811862569726 chr6 171115067 2786655 0.01628526960749751 7.777237483852359 chr7 159138663 4062131 0.025525732863546806 7.521416130728429 chr8 146364022 2140158 0.014622158989317744 5.90546866257465 chr9 141213431 1514547 0.010725233352626352 4.710373967462897 chr10 135534747 2378947 0.017552303395674616 6.967035592184364 chr11 135006516 3150019 0.023332347899415462 5.4597323309294605 chr12 133851895 4086637 0.03053103581387473 7.849604051216565 chr13 115169878 2570646 0.022320471677498867 6.217204630379494 chr14 107349540 488704 0.004552455464643817 2.3051712964574675 chr15 102531392 958968 0.009352920908359461 2.537908221805545 chr16 90354753 1137219 0.012586155816285614 4.142162830947355 chr17 81195210 1486591 0.018308850977785514 6.834982664693756 chr18 78077248 833521 0.010675593996345772 3.20189377992206 chr19 59128983 516338 0.008732401164417118 2.6911859912986826 chr20 63025520 983565 0.01560582126097492 5.333574943714598 chr21 48129895 230881 0.004797039345296723 0.9313135888675814 chr22 51304566 388627 0.0075749008382606725 1.8292293256345913 chrMT 16571 4000088 241.39086355681613 979.2363342622039 chrX 155270560 1807886 0.011643456428572164 3.6379028017215376 chrY 59373566 750500 0.012640305283330969 3.278629525100715