BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084890.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 = 2,885,239 number of mapped reads = 2,598,114 (90.05%) number of supplementary alignments = 16,887 (0.59%) number of secondary alignments = 0 number of mapped bases = 180,226,775 bp number of sequenced bases = 180,158,390 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,231 duplication rate = 3.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5372 >>>>>>> ACTG content number of A's = 52,583,046 bp (29.19%) number of C's = 32,869,907 bp (18.25%) number of T's = 57,702,260 bp (32.03%) number of G's = 36,975,327 bp (20.52%) number of N's = 27,850 bp (0.02%) GC percentage = 38.77% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,514,147 number of insertions = 14,728 mapped reads with insertion percentage = 0.56% number of deletions = 38,922 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.4919X There is a 4.88% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.12% 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 15132468 0.0607118567620339 0.92764188332221 chr2 243199373 16048681 0.06598981239972193 0.5291983866489681 chr3 198022430 13179735 0.06655677844171491 0.29570174923391446 chr4 191154276 11139909 0.058277058892472804 0.28141393468113163 chr5 180915260 10407136 0.0575249207833546 0.2893975720302041 chr6 171115067 11185944 0.06537088870146075 0.3028916106447896 chr7 159138663 11623456 0.07303979925984423 0.45328306323352957 chr8 146364022 8215559 0.0561310005542209 0.9427230953811311 chr9 141213431 11606833 0.08219354857258585 0.528202664001736 chr10 135534747 5594424 0.041276677190388675 0.3449463519982747 chr11 135006516 7625030 0.056478977651715716 0.36716332082436615 chr12 133851895 9013822 0.067341758590717 0.3055950896728737 chr13 115169878 3947867 0.03427864185112708 0.2083465537257546 chr14 107349540 3760548 0.03503087204658725 0.23839768331532954 chr15 102531392 5021531 0.048975546923229134 0.2521318796920509 chr16 90354753 3246096 0.03592612333299168 0.26591566043236536 chr17 81195210 4364851 0.05375749382260357 0.2899768603396241 chr18 78077248 6894644 0.08830541773193645 0.9518335675767411 chr19 59128983 3313902 0.05604530691826714 0.5676980703861569 chr20 63025520 3483250 0.05526729489895522 0.28641692824622544 chr21 48129895 1723670 0.035812876799336466 0.24430635287671504 chr22 51304566 1557466 0.03035725904006283 0.1948899951433007 chrMT 16571 27887 1.6828797296481806 1.629854502393649 chrX 155270560 11697362 0.07533535011402033 0.3511382606306633 chrY 59373566 414704 0.006984657111550281 0.24580930430913941