BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960909.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 = 137,969,456 number of mapped reads = 131,113,548 (95.03%) number of supplementary alignments = 2,144,276 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 65,850,770 number of mapped paired reads (second in pair) = 65,262,778 number of mapped paired reads (both in pair) = 128,107,312 number of mapped paired reads (singletons) = 3,006,236 number of mapped bases = 11,341,921,748 bp number of sequenced bases = 11,338,841,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,815,245 duplication rate = 5.82% >>>>>>> Insert size mean insert size = 161,133.7653 std insert size = 4,152,678.6829 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.3183 >>>>>>> ACTG content number of A's = 3,291,909,745 bp (29.03%) number of C's = 2,328,636,594 bp (20.54%) number of T's = 3,366,457,300 bp (29.69%) number of G's = 2,351,017,336 bp (20.73%) number of N's = 821,017 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 181,711,970 number of insertions = 1,719,331 mapped reads with insertion percentage = 1.28% number of deletions = 1,455,192 mapped reads with deletion percentage = 1.08% homopolymer indels = 36.88% >>>>>>> Coverage mean coverageData = 3.6638X std coverageData = 50.1323X There is a 83.99% of reference with a coverageData >= 1X There is a 71.74% of reference with a coverageData >= 2X There is a 56.96% of reference with a coverageData >= 3X There is a 42.8% of reference with a coverageData >= 4X There is a 30.63% of reference with a coverageData >= 5X There is a 21.12% of reference with a coverageData >= 6X There is a 14.12% of reference with a coverageData >= 7X There is a 9.23% of reference with a coverageData >= 8X There is a 5.93% of reference with a coverageData >= 9X There is a 3.78% of reference with a coverageData >= 10X There is a 2.4% of reference with a coverageData >= 11X There is a 1.54% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.67% of reference with a coverageData >= 14X There is a 0.47% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% 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 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1047262950 4.201646302016636 126.23897116741678 chr2 243199373 985022429 4.050267140285761 74.33526097137248 chr3 198022430 785038750 3.9643930740573174 8.11360669698989 chr4 191154276 687814008 3.5982140833721137 21.91503188678641 chr5 180915260 554234395 3.0635027415597778 4.9646280244708025 chr6 171115067 566916066 3.313069245971192 15.395171824151435 chr7 159138663 642040257 4.034470598763294 32.596776507673106 chr8 146364022 590186305 4.032318167643685 41.29735849112145 chr9 141213431 541825050 3.836922919888548 37.899137764981944 chr10 135534747 548161492 4.0444351292440155 82.66087877999867 chr11 135006516 513745394 3.8053377660675283 24.245763186678115 chr12 133851895 423929627 3.1671544657623265 4.553972023128389 chr13 115169878 355075564 3.083059304794957 3.1473712693151414 chr14 107349540 250272475 2.331379109775412 21.01189335330897 chr15 102531392 295222640 2.8793390418419365 3.685195824875932 chr16 90354753 397667066 4.401174844670319 41.94066950507202 chr17 81195210 224478824 2.7646806258645062 12.437463865902375 chr18 78077248 439062607 5.623438559207415 46.60693687734044 chr19 59128983 225340649 3.8110016030547995 56.494585834580704 chr20 63025520 211607508 3.357489283706029 10.270471292729015 chr21 48129895 160420318 3.333070184341769 15.06416826819457 chr22 51304566 118315676 2.3061431998079858 3.50705927183635 chrMT 16571 2328684 140.5276688190212 30.871936731120297 chrX 155270560 740427541 4.768628006493955 16.448609035735647 chrY 59373566 35525473 0.5983382066019076 26.744858809750106