BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716776.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,626,523 number of mapped reads = 3,353,010 (92.46%) number of supplementary alignments = 68,079 (1.88%) number of secondary alignments = 0 number of mapped bases = 258,432,313 bp number of sequenced bases = 258,334,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,895 duplication rate = 6.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3102 >>>>>>> ACTG content number of A's = 63,160,260 bp (24.45%) number of C's = 54,957,537 bp (21.27%) number of T's = 77,903,801 bp (30.16%) number of G's = 62,303,782 bp (24.12%) number of N's = 9,489 bp (0%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,753,308 number of insertions = 21,466 mapped reads with insertion percentage = 0.63% number of deletions = 47,378 mapped reads with deletion percentage = 1.39% homopolymer indels = 39.86% >>>>>>> Coverage mean coverageData = 0.0835X std coverageData = 0.6318X There is a 6.08% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 29153255 0.11696362032333713 1.2861285764986818 chr2 243199373 24148849 0.09929651011065724 0.6681323522180546 chr3 198022430 16867103 0.0851777397136274 0.3887978120374916 chr4 191154276 12684677 0.0663583220079262 0.5320524778806776 chr5 180915260 13409264 0.0741190323027477 0.3635973707290755 chr6 171115067 15789744 0.09227559137150676 0.44093651201672 chr7 159138663 16505209 0.10371589586623585 0.8212022026229272 chr8 146364022 16006425 0.10936037956103721 0.6077951877406218 chr9 141213431 7738236 0.05479815868222903 0.433190865284973 chr10 135534747 13291008 0.09806347297789253 0.8915144290883696 chr11 135006516 7577959 0.05613032040616469 0.4542304555739694 chr12 133851895 9663004 0.0721917609011064 0.35527353818730484 chr13 115169878 4873594 0.0423165682262857 0.2655779912608938 chr14 107349540 4657146 0.04338300844139621 0.3087661513682166 chr15 102531392 5395678 0.052624643972452846 0.30274880255115055 chr16 90354753 7844098 0.08681444793501898 0.43499313271118156 chr17 81195210 6454364 0.0794919306200452 0.4284104627698045 chr18 78077248 7756640 0.09934571464404074 0.6605674964398229 chr19 59128983 6534363 0.1105103228310218 0.9622887577175123 chr20 63025520 7001070 0.11108309776738058 0.4809508177151535 chr21 48129895 3971374 0.08251366432442872 0.5074423684499149 chr22 51304566 4110818 0.08012577282107795 0.3893901281091208 chrMT 16571 162578 9.81099511194255 6.9722887379823035 chrX 155270560 16002804 0.10306399358642102 0.4581497903964006 chrY 59373566 833053 0.014030705179473303 0.4745498194398056