BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089755.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 = 26,899,906 number of mapped reads = 21,763,273 (80.9%) number of supplementary alignments = 1,093 (0%) number of secondary alignments = 0 number of mapped bases = 1,026,305,432 bp number of sequenced bases = 1,026,113,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,393,125 duplication rate = 12.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4955 >>>>>>> ACTG content number of A's = 305,992,608 bp (29.82%) number of C's = 211,680,380 bp (20.63%) number of T's = 287,588,302 bp (28.03%) number of G's = 220,728,738 bp (21.51%) number of N's = 123,930 bp (0.01%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 4,356,165 number of insertions = 40,314 mapped reads with insertion percentage = 0.19% number of deletions = 124,870 mapped reads with deletion percentage = 0.57% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.3315X std coverageData = 2.2325X There is a 10.33% of reference with a coverageData >= 1X There is a 6.1% of reference with a coverageData >= 2X There is a 4.12% of reference with a coverageData >= 3X There is a 2.94% of reference with a coverageData >= 4X There is a 2.15% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 1.21% of reference with a coverageData >= 7X There is a 0.92% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 83725797 0.33591008385090443 3.299003848739275 chr2 243199373 88117818 0.36232748840187184 2.359881487129967 chr3 198022430 69334127 0.3501326945639441 1.49205911527383 chr4 191154276 62637814 0.32768199231912554 1.68682592371022 chr5 180915260 58176858 0.3215696564236759 1.4395957878478185 chr6 171115067 63646664 0.3719524242713238 1.6875051811750166 chr7 159138663 56336948 0.35401169607664734 3.1483593414627866 chr8 146364022 48085918 0.3285364623281533 4.059855428489605 chr9 141213431 41817078 0.2961267756464327 1.9227469308938319 chr10 135534747 53899958 0.3976836877114619 2.344878550816306 chr11 135006516 48380632 0.3583577551175382 2.165301631654204 chr12 133851895 47217127 0.35275650748164605 1.5758045218194658 chr13 115169878 29434193 0.25557197342867727 1.2893369219419275 chr14 107349540 29575334 0.27550499051975447 1.474415363436831 chr15 102531392 28443833 0.2774158474313896 1.3408006369681058 chr16 90354753 29726952 0.32900263697251214 1.5523315869015737 chr17 81195210 29382178 0.36187082957233563 1.7421420935282823 chr18 78077248 25610698 0.32801742704865827 3.1586285433750056 chr19 59128983 22297944 0.3771068411577449 2.719367798915847 chr20 63025520 22327304 0.35425814812793294 1.610358048098983 chr21 48129895 13749395 0.2856726572954294 1.674905872429926 chr22 51304566 13221432 0.25770478206559627 1.2882255854633364 chrMT 16571 492191 29.70194918834108 20.67090722337188 chrX 155270560 57349361 0.3693511571028017 1.7376431179937473 chrY 59373566 3317878 0.05588140015036321 1.4304734611027439