BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819073.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,658,455 number of mapped reads = 1,504,105 (90.69%) number of supplementary alignments = 5,020 (0.3%) number of secondary alignments = 0 number of mapped bases = 86,001,735 bp number of sequenced bases = 85,979,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,802 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5817 >>>>>>> ACTG content number of A's = 20,178,804 bp (23.47%) number of C's = 17,824,878 bp (20.73%) number of T's = 27,123,961 bp (31.55%) number of G's = 20,850,211 bp (24.25%) number of N's = 1,741 bp (0%) GC percentage = 44.98% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 419,189 number of insertions = 4,472 mapped reads with insertion percentage = 0.3% number of deletions = 13,017 mapped reads with deletion percentage = 0.86% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0278X std coverageData = 0.2225X There is a 2.5% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 9584549 0.0384534608641958 0.32093523494770015 chr2 243199373 7197944 0.029596885514996785 0.2578555775837759 chr3 198022430 5654000 0.028552321067870947 0.18383633516326697 chr4 191154276 5462309 0.028575395300076887 0.19706392648298413 chr5 180915260 4257922 0.02353544969064522 0.16928397696530428 chr6 171115067 4527552 0.026459107776873908 0.18958952415486433 chr7 159138663 3686366 0.02316449020311299 0.19868142888453408 chr8 146364022 5430419 0.03710214385882345 0.24148038631354166 chr9 141213431 3164156 0.02240690547346024 0.22621328054318135 chr10 135534747 4075433 0.03006928547998101 0.22982595270910633 chr11 135006516 2715343 0.020112681079778403 0.20584399416897106 chr12 133851895 3877047 0.028965200679452466 0.18877214667109962 chr13 115169878 2644592 0.022962531921758223 0.16440441252459617 chr14 107349540 3001675 0.027961694106933294 0.19322594113049116 chr15 102531392 2481981 0.024207035051274833 0.16944018660760146 chr16 90354753 2589204 0.028655980056743666 0.1989822253526684 chr17 81195210 1925375 0.02371291360660315 0.17214425474687084 chr18 78077248 2130938 0.02729268838983669 0.39661933106898206 chr19 59128983 1676867 0.028359476434762967 0.257883550959594 chr20 63025520 2722261 0.043192995472310265 0.23443275950761308 chr21 48129895 1103308 0.022923548867081468 0.17666712867445328 chr22 51304566 1059391 0.020649058799171987 0.15685555273189505 chrMT 16571 1005 0.06064812021000543 0.2767486616089286 chrX 155270560 4796044 0.030888302328528988 0.2137318901136229 chrY 59373566 236054 0.003975742336244382 0.09318619512303077