BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237298.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 = 2,464,821 number of mapped reads = 1,958,513 (79.46%) number of supplementary alignments = 14,295 (0.58%) number of secondary alignments = 0 number of mapped bases = 134,213,033 bp number of sequenced bases = 134,141,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,243 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6011 >>>>>>> ACTG content number of A's = 39,006,492 bp (29.08%) number of C's = 25,024,835 bp (18.66%) number of T's = 41,883,433 bp (31.22%) number of G's = 28,224,315 bp (21.04%) number of N's = 2,150 bp (0%) GC percentage = 39.7% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,055,166 number of insertions = 10,425 mapped reads with insertion percentage = 0.53% number of deletions = 40,451 mapped reads with deletion percentage = 2.04% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.4564X There is a 2.93% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 12102046 0.04855372456624692 0.9029918028030122 chr2 243199373 11264281 0.04631706431249722 0.42279970141457185 chr3 198022430 10024563 0.05062337130192777 0.32053472500321695 chr4 191154276 8836274 0.04622587673633835 0.3329318670075436 chr5 180915260 9610062 0.05311913433946921 0.32518371121223205 chr6 171115067 8616750 0.05035646568750138 0.39278439675847987 chr7 159138663 7213739 0.04532989572747636 0.5260938864099123 chr8 146364022 8442888 0.05768417596504693 0.6266149837948062 chr9 141213431 5815184 0.04118010559491328 0.3874873758982444 chr10 135534747 5523066 0.0407501848953907 0.4753563661073746 chr11 135006516 7068104 0.0523537989825617 0.4154076397673855 chr12 133851895 4111202 0.030714559551062014 0.24965212560779315 chr13 115169878 4281757 0.03717775059204283 0.2668744437674805 chr14 107349540 4173897 0.03888136828532288 0.29175414948237854 chr15 102531392 3197107 0.03118173797933027 0.24553983656291986 chr16 90354753 3642191 0.04030989935858715 0.3098711413308688 chr17 81195210 3045595 0.03750954027953127 0.30281756992251285 chr18 78077248 3649085 0.04673685476209408 0.7040260379011731 chr19 59128983 2172629 0.03674389258479213 0.5744503021605338 chr20 63025520 2314408 0.03672175969353367 0.2746704843115153 chr21 48129895 1663638 0.03456558548486341 0.2978672578516428 chr22 51304566 1480634 0.028859692527171948 0.23039882349863589 chrMT 16571 107902 6.51149598696518 4.786373867319727 chrX 155270560 5509932 0.03548600584682634 0.28100727896878963 chrY 59373566 346099 0.005829176573291892 0.21676888816875312