BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053673.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 5,768,677 number of mapped reads = 4,570,163 (79.22%) number of supplementary alignments = 120 (0%) number of secondary alignments = 0 number of mapped bases = 215,055,296 bp number of sequenced bases = 215,014,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 864,699 duplication rate = 13.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4045 >>>>>>> ACTG content number of A's = 62,312,762 bp (28.98%) number of C's = 43,414,474 bp (20.19%) number of T's = 62,211,450 bp (28.93%) number of G's = 46,979,361 bp (21.85%) number of N's = 96,318 bp (0.04%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,511,424 number of insertions = 9,778 mapped reads with insertion percentage = 0.21% number of deletions = 28,848 mapped reads with deletion percentage = 0.63% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0695X std coverageData = 0.5939X There is a 3.6% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 16779310 0.06731902986913722 0.6127574627068723 chr2 243199373 18129266 0.07454487146231253 0.6632588808854736 chr3 198022430 15462463 0.07808440185286081 0.5949457100306352 chr4 191154276 13234467 0.06923448053027075 0.5706056416853355 chr5 180915260 13924162 0.07696510509948139 0.5920427784285168 chr6 171115067 12238164 0.07152008420158583 0.6226158863926409 chr7 159138663 11367212 0.07142960601598117 0.6398419205697305 chr8 146364022 11831706 0.08083752986782503 0.6668583696198179 chr9 141213431 9282132 0.06573122637321942 0.5555089803873008 chr10 135534747 10008470 0.07384431093526149 0.610021213170342 chr11 135006516 9705156 0.07188657471910467 0.6107837578864724 chr12 133851895 10107081 0.07550943526051686 0.5887600630200307 chr13 115169878 7267299 0.06310069200559543 0.5315616021730818 chr14 107349540 6694182 0.0623587394971604 0.5682602478758689 chr15 102531392 5984898 0.05837137176485422 0.5103957032937516 chr16 90354753 6526850 0.07223582360963346 0.5823787846883536 chr17 81195210 5456343 0.06720030652054475 0.5307870883729149 chr18 78077248 5969157 0.0764519389822756 0.6339747396369657 chr19 59128983 3751625 0.0634481570569208 0.615500069471173 chr20 63025520 4517161 0.0716719354318695 0.599640532382655 chr21 48129895 2779602 0.05775208942383938 0.5639170719251589 chr22 51304566 2352125 0.04584630927391531 0.42673358155430047 chrMT 16571 20237 1.2212298593929154 2.180523619957019 chrX 155270560 11143524 0.07176842796213267 0.6049561629230693 chrY 59373566 522704 0.008803648411483319 0.20955241597726154