BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013227.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 = 1,291,513 number of mapped reads = 1,065,115 (82.47%) number of supplementary alignments = 11,285 (0.87%) number of secondary alignments = 0 number of mapped bases = 66,075,653 bp number of sequenced bases = 66,043,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,137 duplication rate = 16.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5079 >>>>>>> ACTG content number of A's = 18,089,178 bp (27.39%) number of C's = 11,661,978 bp (17.66%) number of T's = 21,532,797 bp (32.6%) number of G's = 14,751,987 bp (22.34%) number of N's = 7,128 bp (0.01%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 496,733 number of insertions = 4,394 mapped reads with insertion percentage = 0.41% number of deletions = 18,874 mapped reads with deletion percentage = 1.75% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.3306X There is a 0.83% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 3186815 0.012785584995593652 0.2924811081961064 chr2 243199373 11627070 0.047808799243902654 0.5088712157194022 chr3 198022430 2955553 0.014925344568289561 0.2576088577392862 chr4 191154276 8401980 0.04395392128188647 0.4680729606410271 chr5 180915260 5304657 0.02932122475461716 0.3748467765342522 chr6 171115067 2203744 0.01287872563553974 0.24534135333697943 chr7 159138663 3373508 0.021198544316034625 0.3278235672785762 chr8 146364022 4102005 0.02802604727547047 0.40451420909804636 chr9 141213431 1381011 0.009779600921954797 0.2076550408531594 chr10 135534747 4272595 0.031523982554820425 0.3990992105091633 chr11 135006516 1427386 0.010572719319710464 0.21049913521734617 chr12 133851895 1724338 0.012882432482558428 0.25059867814309256 chr13 115169878 1357297 0.01178517355032711 0.22919875548226626 chr14 107349540 1012324 0.009430166165593258 0.20860466580811263 chr15 102531392 1211827 0.011819082686403009 0.2266076641250987 chr16 90354753 2892500 0.03201270441190847 0.3951902241076619 chr17 81195210 1462468 0.01801175217109482 0.275772324637085 chr18 78077248 1703399 0.021816842212471422 0.34917036425079956 chr19 59128983 783954 0.013258371110492464 0.374456516669842 chr20 63025520 1959215 0.031086058472821802 0.3790890227655276 chr21 48129895 822047 0.017079758848424664 0.2741083106387094 chr22 51304566 421235 0.008210477796459675 0.18111200836657762 chrMT 16571 108191 6.528936093174823 5.440877700127647 chrX 155270560 2266803 0.014599052131968868 0.2506069389605927 chrY 59373566 113731 0.0019155157364137434 0.07302855095597534