BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013337.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 = 2,254,521 number of mapped reads = 1,875,104 (83.17%) number of supplementary alignments = 29,087 (1.29%) number of secondary alignments = 0 number of mapped bases = 119,580,200 bp number of sequenced bases = 119,501,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,357 duplication rate = 9.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4806 >>>>>>> ACTG content number of A's = 32,592,144 bp (27.27%) number of C's = 21,963,890 bp (18.38%) number of T's = 38,018,420 bp (31.81%) number of G's = 26,914,354 bp (22.52%) number of N's = 12,849 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,037,387 number of insertions = 8,567 mapped reads with insertion percentage = 0.45% number of deletions = 45,718 mapped reads with deletion percentage = 2.4% homopolymer indels = 43.56% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3958X There is a 2.35% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 8126584 0.03260406721313645 0.47519526466176865 chr2 243199373 14319280 0.0588787702178821 0.5694024166667109 chr3 198022430 7349587 0.03711492177931561 0.2876580532776665 chr4 191154276 13633085 0.071319801394346 0.4204179758890999 chr5 180915260 4882813 0.026989503262466637 0.24247055911884505 chr6 171115067 6315697 0.03690906423804281 0.34234398071601285 chr7 159138663 2040939 0.012824909808372588 0.22160999300129108 chr8 146364022 7567746 0.0517049606630788 0.5619198311380759 chr9 141213431 5829505 0.041281519461133974 0.43440383000004773 chr10 135534747 3649267 0.026924955266268362 0.3789518123686319 chr11 135006516 3989708 0.02955196621768982 0.35135351388654085 chr12 133851895 5143001 0.03842307200805786 0.3019653246822809 chr13 115169878 3872879 0.03362753410227629 0.277524205736714 chr14 107349540 4802809 0.04473991225300081 0.350609297742961 chr15 102531392 1855636 0.018098223030074537 0.19995427764683538 chr16 90354753 3200734 0.035424080014916315 0.3003963382947644 chr17 81195210 5355270 0.06595549170942473 0.4086053855725171 chr18 78077248 1874377 0.02400669910906696 0.7900601381894041 chr19 59128983 2782189 0.04705288098731548 0.4135510404492537 chr20 63025520 3879922 0.06156112635008803 0.3870595563248764 chr21 48129895 1954347 0.040605677614713266 0.31729910051513366 chr22 51304566 2433343 0.047429365253767085 0.3294659416314432 chrMT 16571 8591 0.5184358216160763 0.8513011007532788 chrX 155270560 4440683 0.028599645676553237 0.2718512221590911 chrY 59373566 272208 0.004584666516409003 0.1356292974005874