BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053666.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 = 14,450,119 number of mapped reads = 11,189,187 (77.43%) number of supplementary alignments = 364 (0%) number of secondary alignments = 0 number of mapped bases = 530,149,909 bp number of sequenced bases = 530,041,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,282,844 duplication rate = 20.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3693 >>>>>>> ACTG content number of A's = 159,656,472 bp (30.12%) number of C's = 98,303,998 bp (18.55%) number of T's = 163,063,363 bp (30.76%) number of G's = 108,594,937 bp (20.49%) number of N's = 422,979 bp (0.08%) GC percentage = 39.03% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 3,156,067 number of insertions = 23,153 mapped reads with insertion percentage = 0.21% number of deletions = 72,733 mapped reads with deletion percentage = 0.65% homopolymer indels = 49.18% >>>>>>> Coverage mean coverageData = 0.1713X std coverageData = 1.2652X There is a 5.94% of reference with a coverageData >= 1X There is a 2.9% of reference with a coverageData >= 2X There is a 1.85% of reference with a coverageData >= 3X There is a 1.28% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% 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 0.05% of reference with a coverageData >= 22X There is a 0.04% 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 0.01% 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 0.01% 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% 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 41393822 0.16607309475870874 1.3315950076481065 chr2 243199373 45355109 0.18649352767862604 1.400558516854493 chr3 198022430 37429379 0.1890158554260747 1.2709075279771493 chr4 191154276 36255759 0.18966752802328105 1.3538973967146049 chr5 180915260 33127646 0.18311139701537615 1.2342239185910056 chr6 171115067 32136935 0.18780891457091853 1.2994870501971834 chr7 159138663 28729162 0.18052911503975624 1.2968002624051187 chr8 146364022 27003404 0.18449482072855308 1.348191798904161 chr9 141213431 21109945 0.14948964025950195 1.148017409418953 chr10 135534747 24319297 0.17943219387128823 1.2969181214465086 chr11 135006516 23816402 0.17640927790477906 1.319530243779336 chr12 133851895 24603819 0.18381375175898704 1.235376658506229 chr13 115169878 18170587 0.15777204348518978 1.223426274251579 chr14 107349540 16335973 0.15217552865154335 1.2424692983848575 chr15 102531392 14900570 0.1453269063195787 1.0708810635268589 chr16 90354753 14139209 0.15648550331381017 1.1472119239628107 chr17 81195210 12681003 0.15617920071886013 1.1008336107745627 chr18 78077248 14246125 0.18246192539982967 1.3908227865480125 chr19 59128983 8671664 0.14665674192299233 1.1644431878748194 chr20 63025520 10523710 0.1669753775930766 1.1617546977878122 chr21 48129895 6925793 0.14389794534145567 1.1571354782949665 chr22 51304566 4540868 0.08850806768348844 0.8002298689286617 chrMT 16571 64658 3.9018767726751555 11.439447310953515 chrX 155270560 32423520 0.2088194954664941 1.416752857908913 chrY 59373566 1245550 0.020978190866959213 0.43273019760735293