BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617395.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,603,877 (92.51%) number of supplementary alignments = 437,222 (1.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,879,397 number of mapped paired reads (second in pair) = 14,724,480 number of mapped paired reads (both in pair) = 29,044,098 number of mapped paired reads (singletons) = 559,779 number of mapped bases = 2,908,298,986 bp number of sequenced bases = 2,907,678,541 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,329,603 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 47,574.2366 std insert size = 2,080,619.6738 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.8597 >>>>>>> ACTG content number of A's = 869,076,352 bp (29.89%) number of C's = 583,085,103 bp (20.05%) number of T's = 858,509,554 bp (29.53%) number of G's = 594,918,854 bp (20.46%) number of N's = 2,088,678 bp (0.07%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 35,220,238 number of insertions = 829,071 mapped reads with insertion percentage = 2.78% number of deletions = 278,550 mapped reads with deletion percentage = 0.92% homopolymer indels = 35.09% >>>>>>> Coverage mean coverageData = 0.9395X std coverageData = 2.874X There is a 29.38% of reference with a coverageData >= 1X There is a 16.82% of reference with a coverageData >= 2X There is a 10.74% of reference with a coverageData >= 3X There is a 7.41% of reference with a coverageData >= 4X There is a 5.37% of reference with a coverageData >= 5X There is a 4.04% of reference with a coverageData >= 6X There is a 3.12% of reference with a coverageData >= 7X There is a 2.46% of reference with a coverageData >= 8X There is a 1.98% of reference with a coverageData >= 9X There is a 1.62% of reference with a coverageData >= 10X There is a 1.34% of reference with a coverageData >= 11X There is a 1.12% of reference with a coverageData >= 12X There is a 0.95% of reference with a coverageData >= 13X There is a 0.81% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.6% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.45% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187074451 0.7505475823869663 2.716979030314719 chr2 243199373 290270560 1.1935497876468621 3.0259945052686743 chr3 198022430 245958106 1.2420719511421003 3.3490765520236576 chr4 191154276 140558671 0.7353153376490515 2.2486233726649894 chr5 180915260 186248488 1.029479149520057 2.827729280482431 chr6 171115067 133654996 0.7810825682580015 2.567526913211203 chr7 159138663 217919944 1.3693714644316197 3.1809637268203663 chr8 146364022 128994949 0.8813296275774657 3.2120624365373063 chr9 141213431 116336033 0.8238312190006912 2.570945392487206 chr10 135534747 93160146 0.6873524912397556 2.363063361596159 chr11 135006516 215661651 1.5974166091361102 3.76018634080374 chr12 133851895 138549045 1.0350921441941483 2.7204012123648593 chr13 115169878 126625974 1.0994712871016499 2.722438399263635 chr14 107349540 84195854 0.7843149956674244 2.835363394538328 chr15 102531392 66578112 0.6493436858830514 2.304955484323609 chr16 90354753 72859136 0.8063674967934449 3.2308680404316563 chr17 81195210 88932007 1.0952863721887043 3.634269960123835 chr18 78077248 41780086 0.5351121750602685 1.9644492843786798 chr19 59128983 40961524 0.6927486643901858 2.2698866579375063 chr20 63025520 98591698 1.5643139160137036 4.625297907439576 chr21 48129895 39909215 0.8291980483231888 2.500240578184869 chr22 51304566 23120015 0.4506424437934043 2.0266828306339124 chrMT 16571 177995 10.741355379880515 4.790526989768818 chrX 155270560 127879220 0.8235896102905792 2.5241592123693053 chrY 59373566 2301110 0.03875647287211956 0.5506314502533202