BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013366.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,161,507 number of mapped reads = 1,937,184 (89.62%) number of supplementary alignments = 9,688 (0.45%) number of secondary alignments = 0 number of mapped bases = 131,169,799 bp number of sequenced bases = 131,111,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,898 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2242 >>>>>>> ACTG content number of A's = 37,802,288 bp (28.83%) number of C's = 23,891,687 bp (18.22%) number of T's = 41,617,712 bp (31.74%) number of G's = 27,771,325 bp (21.18%) number of N's = 28,038 bp (0.02%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,074,606 number of insertions = 10,315 mapped reads with insertion percentage = 0.53% number of deletions = 33,723 mapped reads with deletion percentage = 1.72% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.5417X There is a 3.56% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10171908 0.04080996050958686 0.9361200527468228 chr2 243199373 12216510 0.050232489703005936 0.5876999328746757 chr3 198022430 11808000 0.05962960862564912 0.27804013603263106 chr4 191154276 9178759 0.04801754473962173 0.2871368681364373 chr5 180915260 6242140 0.034503114883730646 0.2156400015889682 chr6 171115067 7354676 0.04298087905958626 0.35651459817503844 chr7 159138663 8973423 0.05638744746774704 1.19439630040745 chr8 146364022 7555726 0.05162283665585522 0.563801400122072 chr9 141213431 5972439 0.04229370363503171 0.4944786326781479 chr10 135534747 5431625 0.04007551657583424 0.632622623860339 chr11 135006516 4619223 0.03421481523158482 0.3581725355784159 chr12 133851895 6782981 0.05067527060412555 0.27308796405092167 chr13 115169878 2602559 0.022597566700556893 0.16977016252998872 chr14 107349540 5155746 0.048027648744465974 0.282643851947406 chr15 102531392 2625849 0.025610195558449064 0.18377663349284418 chr16 90354753 3154162 0.03490864503829699 0.2717134995889866 chr17 81195210 4143418 0.05103032555738202 0.3035044367801158 chr18 78077248 3495840 0.04477411908780391 0.9770745612006144 chr19 59128983 2007536 0.033951810062418965 0.7066425381821156 chr20 63025520 2356306 0.03738653802459702 0.23550880232510504 chr21 48129895 1498750 0.03113968979155263 0.23467520559537217 chr22 51304566 1454294 0.02834628793078573 0.18810176005632565 chrMT 16571 59191 3.5719630680103798 2.704081587804576 chrX 155270560 6043431 0.038921937294487764 0.27036787672391777 chrY 59373566 265307 0.004468436340845689 0.15998559625691944