BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089709.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 = 22,981,645 number of mapped reads = 19,752,491 (85.95%) number of supplementary alignments = 123,179 (0.54%) number of secondary alignments = 0 number of mapped bases = 1,306,406,699 bp number of sequenced bases = 1,305,957,639 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,077,692 duplication rate = 15.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3356 >>>>>>> ACTG content number of A's = 346,826,477 bp (26.56%) number of C's = 244,363,741 bp (18.71%) number of T's = 408,264,520 bp (31.26%) number of G's = 305,993,043 bp (23.43%) number of N's = 509,858 bp (0.04%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 8,396,523 number of insertions = 84,770 mapped reads with insertion percentage = 0.42% number of deletions = 256,420 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.422X std coverageData = 2.9162X There is a 10.7% of reference with a coverageData >= 1X There is a 6.96% of reference with a coverageData >= 2X There is a 5.03% of reference with a coverageData >= 3X There is a 3.79% of reference with a coverageData >= 4X There is a 2.92% of reference with a coverageData >= 5X There is a 2.29% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.45% of reference with a coverageData >= 8X There is a 1.17% of reference with a coverageData >= 9X There is a 0.95% of reference with a coverageData >= 10X There is a 0.77% of reference with a coverageData >= 11X There is a 0.62% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 104095408 0.41763349508364916 5.375408734898357 chr2 243199373 110450487 0.45415613386470366 3.600717986418281 chr3 198022430 88574788 0.44729674310127393 1.9197136297995434 chr4 191154276 84954781 0.4444304505121298 2.1090850214663757 chr5 180915260 82885078 0.45814309970314276 1.9630753071270022 chr6 171115067 75806023 0.44301197041871243 2.1627941945732645 chr7 159138663 73981640 0.46488790722088696 3.402447033962977 chr8 146364022 66706231 0.4557556569468964 4.404102046365923 chr9 141213431 53297019 0.3774217411373568 2.49036094867557 chr10 135534747 60621313 0.4472750666661148 2.574432353176223 chr11 135006516 60220960 0.4460596553724859 2.310267178880861 chr12 133851895 55176920 0.41222367453221337 1.9627693408170477 chr13 115169878 43684158 0.3793019386544805 1.771588287043239 chr14 107349540 40225491 0.3747150756305057 1.8562327661599485 chr15 102531392 37096798 0.3618091715754722 1.827350937603796 chr16 90354753 37778987 0.41811842482708134 1.9761242428082673 chr17 81195210 34340138 0.42293305233153533 2.195253280065647 chr18 78077248 36901985 0.47263429418004077 3.8993598111826033 chr19 59128983 23496331 0.3973741777361535 3.6226948448654013 chr20 63025520 28219440 0.4477462462824583 2.0879688233347005 chr21 48129895 17067171 0.3546064457443757 1.9076749254148206 chr22 51304566 15420740 0.30057246756555744 1.671485780609656 chrMT 16571 55934 3.375414881419347 5.3446117936003485 chrX 155270560 71833977 0.46263745683663404 2.0968263075818223 chrY 59373566 3514901 0.0591997623993142 1.4896472784926957