BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960915.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 225,503,192 number of mapped reads = 220,375,591 (97.73%) number of supplementary alignments = 468,023 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 110,744,326 number of mapped paired reads (second in pair) = 109,631,265 number of mapped paired reads (both in pair) = 218,301,890 number of mapped paired reads (singletons) = 2,073,701 number of mapped bases = 21,533,899,524 bp number of sequenced bases = 21,527,653,973 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,181,096 duplication rate = 12.1% >>>>>>> Insert size mean insert size = 18,698.3457 std insert size = 1,270,799.5425 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5714 >>>>>>> ACTG content number of A's = 6,588,518,570 bp (30.6%) number of C's = 4,184,806,029 bp (19.44%) number of T's = 6,585,955,900 bp (30.59%) number of G's = 4,163,485,511 bp (19.34%) number of N's = 4,887,963 bp (0.02%) GC percentage = 38.78% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 298,134,479 number of insertions = 2,589,668 mapped reads with insertion percentage = 1.15% number of deletions = 2,862,945 mapped reads with deletion percentage = 1.26% homopolymer indels = 40.48% >>>>>>> Coverage mean coverageData = 6.9561X std coverageData = 103.2723X There is a 89.44% of reference with a coverageData >= 1X There is a 85.17% of reference with a coverageData >= 2X There is a 78.89% of reference with a coverageData >= 3X There is a 71.09% of reference with a coverageData >= 4X There is a 62.38% of reference with a coverageData >= 5X There is a 53.41% of reference with a coverageData >= 6X There is a 44.72% of reference with a coverageData >= 7X There is a 36.71% of reference with a coverageData >= 8X There is a 29.6% of reference with a coverageData >= 9X There is a 23.51% of reference with a coverageData >= 10X There is a 18.42% of reference with a coverageData >= 11X There is a 14.28% of reference with a coverageData >= 12X There is a 10.98% of reference with a coverageData >= 13X There is a 8.39% of reference with a coverageData >= 14X There is a 6.38% of reference with a coverageData >= 15X There is a 4.85% of reference with a coverageData >= 16X There is a 3.68% of reference with a coverageData >= 17X There is a 2.8% of reference with a coverageData >= 18X There is a 2.14% of reference with a coverageData >= 19X There is a 1.65% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.81% of reference with a coverageData >= 23X There is a 0.66% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.37% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1788851154 7.176917541160309 272.96933296978614 chr2 243199373 1813259435 7.455855714726699 55.098382038744006 chr3 198022430 1600880078 8.084337102620143 9.429905591939287 chr4 191154276 1420875945 7.433137122185014 56.6598358991394 chr5 180915260 1169998058 6.46710541719919 9.257399424131961 chr6 171115067 1131810666 6.614325002718784 27.00948499896555 chr7 159138663 1184806150 7.44511816088338 67.9005711119893 chr8 146364022 1262748272 8.627449934383465 132.8657214424003 chr9 141213431 919332446 6.51023376097986 98.01285159809576 chr10 135534747 1026289145 7.572147864045521 198.85762097162856 chr11 135006516 1049967836 7.777164148136376 43.237102163542296 chr12 133851895 973150964 7.270356269517141 11.463558404525404 chr13 115169878 743142277 6.45257501271296 4.84166610185088 chr14 107349540 457931371 4.265797235833521 7.269623909628792 chr15 102531392 578870796 5.645790861787968 5.106475452731616 chr16 90354753 707403881 7.829182832252333 84.86161034081299 chr17 81195210 411093823 5.06303047926103 26.0872814684655 chr18 78077248 828188232 10.607292818517374 100.46923961934327 chr19 59128983 398717546 6.7431828820732465 114.56391253026918 chr20 63025520 405020998 6.426301567999756 18.498136395175674 chr21 48129895 286854525 5.960007288609294 22.339069867377667 chr22 51304566 221983883 4.326786099311317 5.640680885156573 chrMT 16571 4882317 294.63019733268965 57.70321661525386 chrX 155270560 1088555448 7.010700856620856 28.985069165344527 chrY 59373566 59284278 0.9984961657852924 52.55876094847353