BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089606.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 = 11,183,843 number of mapped reads = 9,302,190 (83.18%) number of supplementary alignments = 386 (0%) number of secondary alignments = 0 number of mapped bases = 437,132,258 bp number of sequenced bases = 437,043,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,552,188 duplication rate = 20.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0214 >>>>>>> ACTG content number of A's = 139,180,152 bp (31.85%) number of C's = 82,569,431 bp (18.89%) number of T's = 120,403,200 bp (27.55%) number of G's = 94,689,169 bp (21.67%) number of N's = 201,365 bp (0.05%) GC percentage = 40.56% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 2,500,655 number of insertions = 18,850 mapped reads with insertion percentage = 0.2% number of deletions = 59,468 mapped reads with deletion percentage = 0.64% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.1412X std coverageData = 1.0665X There is a 5.4% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.57% of reference with a coverageData >= 3X There is a 1.05% of reference with a coverageData >= 4X There is a 0.73% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 34834505 0.13975694367477623 1.1106921416407978 chr2 243199373 36988072 0.15208950394785764 1.279720387468178 chr3 198022430 28367870 0.14325584228008917 0.99232458551441 chr4 191154276 28674327 0.1500062023200569 1.0642589010722237 chr5 180915260 27223744 0.1504778756639987 1.0047794884516652 chr6 171115067 25511341 0.14908880583847126 1.0676651074402206 chr7 159138663 23778763 0.14942165877062824 1.2130010256289003 chr8 146364022 22677989 0.15494237374810593 1.293367687295601 chr9 141213431 18171073 0.12867807878699583 0.970741394214425 chr10 135534747 20314475 0.14988388918452034 1.0574627892747324 chr11 135006516 20048184 0.14849789916806683 1.0957552381884614 chr12 133851895 19926057 0.1488664542253959 0.9934181659118282 chr13 115169878 14627720 0.1270099461249755 0.9400614330720942 chr14 107349540 13689652 0.12752408626995515 1.0263084583176025 chr15 102531392 12446040 0.12138760390573845 0.8859283276972362 chr16 90354753 12047665 0.13333736853887476 0.955536984084928 chr17 81195210 11198814 0.1379245647618868 0.9591362110140286 chr18 78077248 11209532 0.14356976311460157 1.087063688640378 chr19 59128983 7966002 0.13472245920414358 1.0530775623760917 chr20 63025520 9164758 0.14541344522028538 1.0153431874791592 chr21 48129895 5782490 0.12014341606188836 0.9618101955208047 chr22 51304566 4750875 0.09260140705605033 0.7347336599383578 chrMT 16571 110267 6.654215195220566 11.999853501641612 chrX 155270560 26502744 0.17068750186770756 1.153124590332871 chrY 59373566 1119299 0.01885180687984953 0.40653980063374984