BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089377.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 = 25,701,801 number of mapped reads = 24,049,268 (93.57%) number of supplementary alignments = 134,668 (0.52%) number of secondary alignments = 0 number of mapped bases = 1,569,954,908 bp number of sequenced bases = 1,569,398,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,497,610 duplication rate = 14.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3546 >>>>>>> ACTG content number of A's = 401,721,564 bp (25.6%) number of C's = 296,593,799 bp (18.9%) number of T's = 486,638,602 bp (31.01%) number of G's = 384,259,888 bp (24.48%) number of N's = 184,160 bp (0.01%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,445,369 number of insertions = 105,854 mapped reads with insertion percentage = 0.44% number of deletions = 315,570 mapped reads with deletion percentage = 1.3% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.5071X std coverageData = 3.039X There is a 17.4% of reference with a coverageData >= 1X There is a 10.17% of reference with a coverageData >= 2X There is a 6.45% of reference with a coverageData >= 3X There is a 4.28% of reference with a coverageData >= 4X There is a 2.94% of reference with a coverageData >= 5X There is a 2.07% of reference with a coverageData >= 6X There is a 1.49% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 127054898 0.5097475684925175 4.696880328258396 chr2 243199373 130734589 0.5375613735648899 4.049391027207172 chr3 198022430 109061364 0.5507525788871493 1.7687153357974545 chr4 191154276 97242314 0.5087111627050394 2.3838133123801994 chr5 180915260 91996415 0.508505556689911 1.6920847923243891 chr6 171115067 94581656 0.5527371590252774 2.4590468692814507 chr7 159138663 87682265 0.5509802793806304 3.7733321658788412 chr8 146364022 80733262 0.5515922622022508 2.9175844760942256 chr9 141213431 62844225 0.44503008357611534 3.199148115283825 chr10 135534747 73132317 0.5395835283479004 3.8667752929354418 chr11 135006516 75765067 0.5611956314760392 3.220329927140564 chr12 133851895 71713095 0.5357645104688282 1.9202025838187533 chr13 115169878 47686342 0.41405220556020733 1.5110977081656893 chr14 107349540 46809822 0.4360505131181745 1.7467857618947968 chr15 102531392 44657951 0.43555393259461456 1.7584934887437156 chr16 90354753 46591882 0.5156550203839304 2.1962953954339324 chr17 81195210 44860898 0.5525067057527162 2.2957345622087555 chr18 78077248 40780238 0.5223062933775535 6.106972187836425 chr19 59128983 29788087 0.5037814873291495 3.2614825925708155 chr20 63025520 32695231 0.5187617809420692 2.0266808311726763 chr21 48129895 20423026 0.4243314056679326 2.2867953220090596 chr22 51304566 18824836 0.36692320913503096 1.452570597653852 chrMT 16571 130012 7.8457546315853 15.341582058441718 chrX 155270560 90040107 0.5798916871298719 2.3215157569365696 chrY 59373566 4125009 0.06947551373282851 1.7275247156216509