BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549034.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,693,973 number of mapped reads = 6,492,364 (84.38%) number of secondary alignments = 0 number of mapped bases = 257,378,716 bp number of sequenced bases = 257,354,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,493 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1022 >>>>>>> ACTG content number of A's = 74,586,091 bp (28.98%) number of C's = 53,849,614 bp (20.92%) number of T's = 75,057,140 bp (29.16%) number of G's = 53,861,779 bp (20.93%) number of N's = 187 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 652,136 number of insertions = 6,794 mapped reads with insertion percentage = 0.1% number of deletions = 18,134 mapped reads with deletion percentage = 0.28% homopolymer indels = 43.3% >>>>>>> Coverage mean coverageData = 0.0831X std coverageData = 0.5924X There is a 5.88% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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% 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 20784502 0.08338796475857126 0.7385022089884178 chr2 243199373 22747096 0.0935327082442766 0.5565626847812696 chr3 198022430 18257575 0.09219953012393596 0.41171697862942735 chr4 191154276 18149729 0.09494806697392424 0.44648084301498664 chr5 180915260 16137857 0.08920119286786532 0.40922998553544876 chr6 171115067 15445304 0.09026267686877626 0.43566238864665063 chr7 159138663 14201716 0.08924114185878261 0.6690854722630011 chr8 146364022 13277455 0.0907152920408268 1.495501434024736 chr9 141213431 11001119 0.07790419737057447 0.5119723564565801 chr10 135534747 12158585 0.08970825023932792 0.5264378810048276 chr11 135006516 11340129 0.08399690130511923 0.45549084689324426 chr12 133851895 12018490 0.0897894646915533 0.41197669984368546 chr13 115169878 8617795 0.0748268136569529 0.3715837418083628 chr14 107349540 8136277 0.07579237880292733 0.4350287836415591 chr15 102531392 7326385 0.0714550427638786 0.3631428337356012 chr16 90354753 7164579 0.07929388064399888 0.41563114932080286 chr17 81195210 6562975 0.08082958342000716 0.4000763751569111 chr18 78077248 6935539 0.08882919387732519 0.8060498871517671 chr19 59128983 4776491 0.08078087526044546 0.6926722087053561 chr20 63025520 5357652 0.08500766038899799 0.41346502502798566 chr21 48129895 3366803 0.06995242769592579 0.43939219044179695 chr22 51304566 2877410 0.056084871666198285 0.4664748703778714 chrMT 16571 10877 0.6563876651982379 1.023827433103501 chrX 155270560 8349384 0.05377312994813698 0.344986436330084 chrY 59373566 2376992 0.040034516370466955 0.3929089677519185