BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819147.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 = 2,310,285 number of mapped reads = 2,115,791 (91.58%) number of supplementary alignments = 9,492 (0.41%) number of secondary alignments = 0 number of mapped bases = 122,844,990 bp number of sequenced bases = 122,808,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 203,144 duplication rate = 7.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7804 >>>>>>> ACTG content number of A's = 29,156,347 bp (23.74%) number of C's = 22,942,181 bp (18.68%) number of T's = 39,590,310 bp (32.24%) number of G's = 31,118,439 bp (25.34%) number of N's = 1,710 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 611,652 number of insertions = 7,633 mapped reads with insertion percentage = 0.36% number of deletions = 21,569 mapped reads with deletion percentage = 1.01% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.359X There is a 3.06% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11712318 0.04699012565348834 0.6418660556764658 chr2 243199373 9884539 0.04064376843603129 0.44705754898892386 chr3 198022430 7333431 0.03703333506209373 0.2402816212267193 chr4 191154276 7542120 0.039455669827652716 0.28782412760952203 chr5 180915260 6825718 0.03772881292600746 0.2417700717086571 chr6 171115067 5488528 0.03207507144885143 0.2738014488972435 chr7 159138663 5996654 0.03768194282240514 0.4320683437068642 chr8 146364022 10601709 0.07243384579852555 0.4177931832226215 chr9 141213431 5030006 0.03561988377720247 0.28555454284105325 chr10 135534747 6429789 0.04744015200766192 0.38327420523162953 chr11 135006516 4395604 0.03255845814138334 0.3028493148919546 chr12 133851895 5586501 0.041736435632831345 0.2574361643808003 chr13 115169878 2609235 0.022655533246288582 0.1909634480981977 chr14 107349540 3022222 0.02815309688332153 0.21276334638709118 chr15 102531392 3246063 0.031659211258928385 0.22339217219228125 chr16 90354753 3883128 0.04297646632933632 0.27642301992490337 chr17 81195210 4273907 0.05263742774974041 0.3030456244854135 chr18 78077248 2578737 0.033028021172057706 0.48687486790533385 chr19 59128983 2417421 0.040883858935980684 0.4425921032393025 chr20 63025520 3377723 0.05359294139897616 0.2972655688115824 chr21 48129895 1604169 0.03332999168188503 0.254249122023694 chr22 51304566 1032805 0.02013085930792203 0.17949715762997295 chrMT 16571 246048 14.848108140727778 8.686237820402853 chrX 155270560 7316166 0.04711882278263181 0.29093374146249973 chrY 59373566 410449 0.006912992222835327 0.17308761676319268