BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053611.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 = 8,200,574 number of mapped reads = 6,784,407 (82.73%) number of supplementary alignments = 280 (0%) number of secondary alignments = 0 number of mapped bases = 319,953,488 bp number of sequenced bases = 319,887,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,228,919 duplication rate = 13.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8724 >>>>>>> ACTG content number of A's = 94,269,585 bp (29.47%) number of C's = 61,924,979 bp (19.36%) number of T's = 95,922,702 bp (29.99%) number of G's = 67,763,331 bp (21.18%) number of N's = 7,292 bp (0%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,741,109 number of insertions = 13,123 mapped reads with insertion percentage = 0.19% number of deletions = 43,998 mapped reads with deletion percentage = 0.65% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.1034X std coverageData = 0.7154X There is a 5.22% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 25436877 0.10205341474354843 0.7738060017061795 chr2 243199373 26840269 0.11036323272099884 0.8391588271158732 chr3 198022430 21956849 0.11088061589790611 0.6807336622895656 chr4 191154276 21107593 0.11042176738960315 0.7144647097529616 chr5 180915260 19786100 0.10936667255155812 0.6689475182313007 chr6 171115067 18996653 0.1110168340699069 0.7542202778862862 chr7 159138663 17314724 0.10880274895862359 0.7672458984632172 chr8 146364022 16297637 0.1113500215237321 0.7528387162724838 chr9 141213431 13273189 0.09399381422861966 0.6768664585596094 chr10 135534747 14774909 0.10901196428986583 0.7168457853178023 chr11 135006516 14480390 0.10725697121167099 0.7456122524263947 chr12 133851895 14695694 0.109790705615337 0.6798941237498557 chr13 115169878 10435976 0.09061376274098337 0.6110484128748956 chr14 107349540 9883004 0.09206377596028824 0.7308198210575572 chr15 102531392 9224818 0.08997066966573515 0.6061063750942491 chr16 90354753 8925641 0.09878441037849996 0.6625437044674127 chr17 81195210 8318269 0.10244777986287615 0.6361242348053702 chr18 78077248 8503481 0.10891112606837781 0.7701523485167584 chr19 59128983 5810701 0.09827162087330336 0.7540066037830112 chr20 63025520 6810874 0.10806533607338742 0.692952877172201 chr21 48129895 4194751 0.08715479225541631 0.696665434920678 chr22 51304566 3494181 0.068106628170288 0.5174445905255478 chrMT 16571 38581 2.328224005793253 4.2200934891946655 chrX 155270560 18604124 0.11981745927882272 0.7421040890177322 chrY 59373566 748203 0.01260161803318332 0.24978180530413513