BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777248.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 10,009,904 number of mapped reads = 9,530,396 (95.21%) number of supplementary alignments = 468,787 (4.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,783,970 number of mapped paired reads (second in pair) = 4,746,426 number of mapped paired reads (both in pair) = 9,443,502 number of mapped paired reads (singletons) = 86,894 number of mapped bases = 814,543,944 bp number of sequenced bases = 814,122,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,642,466 duplication rate = 14.62% >>>>>>> Insert size mean insert size = 329,549.0847 std insert size = 5,604,290.9148 median insert size = 127 >>>>>>> Mapping quality mean mapping quality = 51.0319 >>>>>>> ACTG content number of A's = 229,410,413 bp (28.18%) number of C's = 156,749,714 bp (19.25%) number of T's = 246,922,206 bp (30.33%) number of G's = 181,025,179 bp (22.24%) number of N's = 14,708 bp (0%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 5,434,352 number of insertions = 86,299 mapped reads with insertion percentage = 0.89% number of deletions = 234,823 mapped reads with deletion percentage = 2.42% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.2631X std coverageData = 2.9486X There is a 13.28% of reference with a coverageData >= 1X There is a 6.78% of reference with a coverageData >= 2X There is a 2.72% of reference with a coverageData >= 3X There is a 1.36% of reference with a coverageData >= 4X There is a 0.65% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% 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 67536672 0.2709588916129521 3.9543670556871415 chr2 243199373 77375843 0.31815806942890434 2.6015475066640192 chr3 198022430 53310341 0.2692136491810549 0.8476932328151295 chr4 191154276 50304436 0.2631614476675374 1.1003929681336668 chr5 180915260 53781132 0.2972725020542767 0.8995071652361989 chr6 171115067 39446736 0.23052754319992172 8.38170996559976 chr7 159138663 55404161 0.34815022292854125 3.1548221272650014 chr8 146364022 40593674 0.2773473524798328 3.973653199796314 chr9 141213431 30261442 0.2142957775737352 2.8873007182626425 chr10 135534747 37457246 0.2763663697251008 2.126129473775995 chr11 135006516 46130528 0.341691122523301 1.8223339060592876 chr12 133851895 37227925 0.2781277396184791 1.22620663885884 chr13 115169878 34483101 0.2994107625954071 0.8957176508223407 chr14 107349540 16557427 0.15423845318759632 0.7507414892704279 chr15 102531392 29638589 0.2890684347677636 0.8911488437957882 chr16 90354753 21669444 0.2398262767648759 1.313516523977747 chr17 81195210 20276996 0.24973143120142186 1.0778605437326172 chr18 78077248 18001587 0.23056123853135807 3.5340201430692426 chr19 59128983 17871558 0.302247004654215 2.6318802955973712 chr20 63025520 20554303 0.32612667059311845 0.9746223286689106 chr21 48129895 7854817 0.16320037681362073 0.8333484833203952 chr22 51304566 6618552 0.12900512597650665 0.5855261931509513 chrMT 16571 1961634 118.37752700500874 65.52622337550942 chrX 155270560 28596110 0.18416955538770519 0.9502588252222302 chrY 59373566 1629690 0.027448073440628443 1.0123172956473494