BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083780.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,799,519 number of mapped reads = 1,757,230 (62.77%) number of supplementary alignments = 11,022 (0.39%) number of secondary alignments = 0 number of mapped bases = 110,619,959 bp number of sequenced bases = 110,583,239 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,981 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2947 >>>>>>> ACTG content number of A's = 31,618,244 bp (28.59%) number of C's = 21,112,343 bp (19.09%) number of T's = 33,504,841 bp (30.3%) number of G's = 24,346,508 bp (22.02%) number of N's = 1,303 bp (0%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 894,424 number of insertions = 8,068 mapped reads with insertion percentage = 0.46% number of deletions = 22,979 mapped reads with deletion percentage = 1.3% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.2727X There is a 3.15% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7432696 0.029820170438010662 0.3908889596686939 chr2 243199373 9392530 0.038620699897939294 0.32878050567618433 chr3 198022430 7730370 0.039037850409168295 0.21784788665832192 chr4 191154276 7597503 0.03974539915601993 0.22723762418480137 chr5 180915260 7476906 0.04132822184264611 0.22488570369988192 chr6 171115067 6508629 0.038036562846917504 0.24616903849316552 chr7 159138663 6318614 0.03970508411271496 0.3271197155641767 chr8 146364022 5792119 0.03957337958367938 0.28197339597346854 chr9 141213431 4374676 0.030979177894204697 0.24478499433175513 chr10 135534747 5068047 0.03739297200296541 0.2873080814668514 chr11 135006516 5446879 0.04034530451848709 0.2557591742330779 chr12 133851895 5112191 0.03819289222614293 0.21688362431217587 chr13 115169878 3618400 0.031417937249182466 0.19593332957063628 chr14 107349540 3367035 0.03136515536070299 0.2025957583273252 chr15 102531392 3289069 0.032078653530813274 0.20041967069645908 chr16 90354753 3089768 0.03419596531905743 0.22214280123447125 chr17 81195210 2660493 0.03276662502627926 0.21736848401138537 chr18 78077248 3082840 0.0394844859286024 0.46544415659601884 chr19 59128983 1043247 0.017643580982950442 0.2957023720591226 chr20 63025520 2291596 0.03635981107335568 0.2141853845868346 chr21 48129895 1387300 0.0288240811661858 0.1960294241813732 chr22 51304566 1054810 0.02055976850091666 0.15723740931706548 chrMT 16571 210746 12.717759942067467 7.7553965893229 chrX 155270560 6975226 0.044923042719753184 0.25102937826839244 chrY 59373566 298269 0.005023599222590066 0.11129718288691623