BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714215.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 159,704 number of mapped reads = 16,650 (10.43%) number of supplementary alignments = 513 (0.32%) number of secondary alignments = 0 number of mapped bases = 1,681,034 bp number of sequenced bases = 1,653,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,833 duplication rate = 37.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 33.8702 >>>>>>> ACTG content number of A's = 346,796 bp (20.97%) number of C's = 234,869 bp (14.21%) number of T's = 309,990 bp (18.75%) number of G's = 761,710 bp (46.07%) number of N's = 18 bp (0%) GC percentage = 60.28% >>>>>>> Mismatches and indels general error rate = 0.0381 number of mismatches = 56,460 number of insertions = 1,745 mapped reads with insertion percentage = 9.23% number of deletions = 4,087 mapped reads with deletion percentage = 23.08% homopolymer indels = 32.54% >>>>>>> Coverage mean coverageData = 0.0005X std coverageData = 0.6207X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 61708 2.475741073479612E-4 0.07600058539942064 chr2 243199373 574892 0.0023638712259344517 2.1730493958314008 chr3 198022430 73343 3.7037723453853185E-4 0.10025777833333999 chr4 191154276 81204 4.248087026836899E-4 0.12555665199125923 chr5 180915260 62495 3.454379691353842E-4 0.09788534332676233 chr6 171115067 51147 2.989041286469531E-4 0.10289457103768025 chr7 159138663 30297 1.9038113949719433E-4 0.09348176652727253 chr8 146364022 50854 3.4744877398900666E-4 0.1349085284906528 chr9 141213431 43728 3.096589303888523E-4 0.07793876519553995 chr10 135534747 63822 4.7089031715239784E-4 0.1660185718622917 chr11 135006516 75622 5.601359270688832E-4 0.17477528120704064 chr12 133851895 26872 2.0075920479123587E-4 0.07535160185735154 chr13 115169878 23998 2.0837045603191488E-4 0.0672629233018323 chr14 107349540 18638 1.7361974722947113E-4 0.053470887083297274 chr15 102531392 13686 1.3348107085096436E-4 0.04367221852031412 chr16 90354753 12946 1.4327967893399034E-4 0.047670166111554765 chr17 81195210 23396 2.88145076538382E-4 0.08393611951622772 chr18 78077248 39199 5.020540682991285E-4 0.1597804308947502 chr19 59128983 5503 9.306772619444512E-5 0.02740765936863338 chr20 63025520 6505 1.0321215913807613E-4 0.030330679762501183 chr21 48129895 12815 2.6625863197914725E-4 0.08320438089718844 chr22 51304566 13986 2.726073153021117E-4 0.13586801370093196 chrMT 16571 0 0.0 0.0 chrX 155270560 308502 0.001986867310841154 0.3148794645194908 chrY 59373566 5876 9.896660072598637E-5 0.047342805612071215