BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975261.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 5,238,886 number of mapped reads = 5,184,991 (98.97%) number of supplementary alignments = 19,088 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,591,263 number of mapped paired reads (second in pair) = 2,593,728 number of mapped paired reads (both in pair) = 5,165,806 number of mapped paired reads (singletons) = 19,185 number of mapped bases = 471,914,430 bp number of sequenced bases = 471,645,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 273,469 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 94,655.5409 std insert size = 2,973,035.5964 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.8924 >>>>>>> ACTG content number of A's = 138,171,333 bp (29.3%) number of C's = 89,856,748 bp (19.05%) number of T's = 141,122,036 bp (29.92%) number of G's = 102,488,443 bp (21.73%) number of N's = 6,673 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 3,613,519 number of insertions = 78,544 mapped reads with insertion percentage = 1.48% number of deletions = 154,043 mapped reads with deletion percentage = 2.91% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.1524X std coverageData = 1.3804X There is a 10.01% of reference with a coverageData >= 1X There is a 3.25% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% of reference with a coverageData >= 27X There is a 0% 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 39362844 0.15792475798886776 1.3439097243503404 chr2 243199373 41743478 0.1716430329777207 1.8256811007514477 chr3 198022430 31247304 0.15779679099988825 0.5639218232089473 chr4 191154276 31055656 0.1624638310471276 1.170640716881185 chr5 180915260 30626964 0.16928900303932348 0.5717262678373719 chr6 171115067 28040205 0.16386753949609825 1.4386371206373822 chr7 159138663 23569969 0.14810963316940773 1.3931380391122625 chr8 146364022 22962208 0.15688423757581627 0.7118451863288873 chr9 141213431 19863865 0.14066555043195572 1.8614711365450627 chr10 135534747 24926762 0.18391418106236623 3.4830641862086407 chr11 135006516 20327270 0.15056510309472768 1.0878856396695584 chr12 133851895 21743853 0.1624471061840402 0.5453486791153055 chr13 115169878 14204815 0.12333793563626072 0.46707575959229314 chr14 107349540 13548314 0.1262074714060256 0.5431048545584061 chr15 102531392 12651003 0.12338663070135632 0.46854074035075627 chr16 90354753 14579727 0.16136093028775145 1.810823731253175 chr17 81195210 11698518 0.1440789179558745 1.521941021813726 chr18 78077248 13604519 0.17424434580481116 2.054787965168484 chr19 59128983 5977462 0.1010919129118118 0.8030432189464667 chr20 63025520 9701812 0.1539346601186313 0.5979835403747427 chr21 48129895 5975378 0.12415107076381529 0.6530272017418456 chr22 51304566 4576645 0.08920541302308259 0.4293386688330304 chrMT 16571 64237 3.8764709432140485 2.920041179588159 chrX 155270560 28581750 0.18407707166123444 0.7981942449333022 chrY 59373566 1279872 0.021556259565073118 1.284804607632111