BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961005.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 = 386,104,440 number of mapped reads = 378,247,355 (97.97%) number of supplementary alignments = 808,621 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,395,680 number of mapped paired reads (second in pair) = 188,851,675 number of mapped paired reads (both in pair) = 377,123,288 number of mapped paired reads (singletons) = 1,124,067 number of mapped bases = 36,932,110,843 bp number of sequenced bases = 36,920,711,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,942,380 duplication rate = 11.97% >>>>>>> Insert size mean insert size = 15,807.6419 std insert size = 1,206,357.4833 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.5871 >>>>>>> ACTG content number of A's = 10,943,233,285 bp (29.64%) number of C's = 7,499,191,622 bp (20.31%) number of T's = 10,888,586,288 bp (29.49%) number of G's = 7,573,140,703 bp (20.51%) number of N's = 16,559,651 bp (0.04%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 204,161,071 number of insertions = 3,795,464 mapped reads with insertion percentage = 0.97% number of deletions = 4,468,470 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 11.9302X std coverageData = 140.8595X There is a 91.21% of reference with a coverageData >= 1X There is a 90.5% of reference with a coverageData >= 2X There is a 88.89% of reference with a coverageData >= 3X There is a 86.72% of reference with a coverageData >= 4X There is a 83.42% of reference with a coverageData >= 5X There is a 79.45% of reference with a coverageData >= 6X There is a 74.52% of reference with a coverageData >= 7X There is a 69.16% of reference with a coverageData >= 8X There is a 63.28% of reference with a coverageData >= 9X There is a 57.32% of reference with a coverageData >= 10X There is a 51.29% of reference with a coverageData >= 11X There is a 45.46% of reference with a coverageData >= 12X There is a 39.87% of reference with a coverageData >= 13X There is a 34.65% of reference with a coverageData >= 14X There is a 29.84% of reference with a coverageData >= 15X There is a 25.48% of reference with a coverageData >= 16X There is a 21.57% of reference with a coverageData >= 17X There is a 18.12% of reference with a coverageData >= 18X There is a 15.11% of reference with a coverageData >= 19X There is a 12.52% of reference with a coverageData >= 20X There is a 10.31% of reference with a coverageData >= 21X There is a 8.45% of reference with a coverageData >= 22X There is a 6.89% of reference with a coverageData >= 23X There is a 5.59% of reference with a coverageData >= 24X There is a 4.53% of reference with a coverageData >= 25X There is a 3.67% of reference with a coverageData >= 26X There is a 2.96% of reference with a coverageData >= 27X There is a 2.39% of reference with a coverageData >= 28X There is a 1.94% of reference with a coverageData >= 29X There is a 1.57% of reference with a coverageData >= 30X There is a 1.28% of reference with a coverageData >= 31X There is a 1.05% of reference with a coverageData >= 32X There is a 0.86% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.6% of reference with a coverageData >= 35X There is a 0.51% of reference with a coverageData >= 36X There is a 0.44% of reference with a coverageData >= 37X There is a 0.38% of reference with a coverageData >= 38X There is a 0.34% of reference with a coverageData >= 39X There is a 0.3% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3188773859 12.793443989052289 338.5779678473707 chr2 243199373 3815178305 15.687451237795749 82.60282773883112 chr3 198022430 2363027804 11.933132039638135 41.95351896884778 chr4 191154276 1966558880 10.287810040932593 115.31720453710919 chr5 180915260 1940604410 10.726593268030568 13.169114189912746 chr6 171115067 2193432978 12.818467809149734 41.128807622025654 chr7 159138663 1900476341 11.942266606827028 87.04827992615817 chr8 146364022 2067925330 14.128645152973455 132.44572288096208 chr9 141213431 1865278670 13.208932442127265 94.20389245260927 chr10 135534747 1629927463 12.025901099737915 347.1619384834629 chr11 135006516 1648752364 12.21239102266738 54.09505307695317 chr12 133851895 1856382434 13.86892904280511 12.74151393810152 chr13 115169878 1002669804 8.706007346816847 7.650273783863881 chr14 107349540 736178559 6.8577709694890165 12.187302408566607 chr15 102531392 933684232 9.106325524186778 7.303463197891534 chr16 90354753 1066937902 11.80832071999577 132.92902899917985 chr17 81195210 896411852 11.04020609097507 36.558205167114714 chr18 78077248 1130091242 14.474014785971965 125.0590973040551 chr19 59128983 769437706 13.012868934343079 171.1255037905348 chr20 63025520 781936672 12.406667521346908 37.18162821250977 chr21 48129895 455452462 9.462984741603945 63.08123659960871 chr22 51304566 512549569 9.9903304707811 11.278791716918692 chrMT 16571 17326817 1045.6108261420554 177.92989758779774 chrX 155270560 2072975149 13.350728876098598 42.28825187446164 chrY 59373566 120140039 2.0234600529131095 124.21847241484329