BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504630.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 = 598,059,300 number of mapped reads = 514,938,517 (86.1%) number of supplementary alignments = 4,491,211 (0.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 262,262,954 number of mapped paired reads (second in pair) = 252,675,563 number of mapped paired reads (both in pair) = 492,232,572 number of mapped paired reads (singletons) = 22,705,945 number of mapped bases = 48,482,222,134 bp number of sequenced bases = 48,442,659,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,324,794 duplication rate = 23.99% >>>>>>> Insert size mean insert size = 102,675.9376 std insert size = 2,977,552.56 median insert size = 353 >>>>>>> Mapping quality mean mapping quality = 51.558 >>>>>>> ACTG content number of A's = 13,179,309,780 bp (27.21%) number of C's = 10,995,431,604 bp (22.7%) number of T's = 13,338,506,029 bp (27.53%) number of G's = 10,903,379,605 bp (22.51%) number of N's = 26,032,787 bp (0.05%) GC percentage = 45.21% >>>>>>> Mismatches and indels general error rate = 0.0259 number of mismatches = 1,202,603,085 number of insertions = 13,298,845 mapped reads with insertion percentage = 2.41% number of deletions = 12,221,971 mapped reads with deletion percentage = 2.22% homopolymer indels = 33.18% >>>>>>> Coverage mean coverageData = 15.6612X std coverageData = 331.6805X There is a 87.4% of reference with a coverageData >= 1X There is a 82.51% of reference with a coverageData >= 2X There is a 77.22% of reference with a coverageData >= 3X There is a 72.08% of reference with a coverageData >= 4X There is a 67.14% of reference with a coverageData >= 5X There is a 62.52% of reference with a coverageData >= 6X There is a 58.2% of reference with a coverageData >= 7X There is a 54.2% of reference with a coverageData >= 8X There is a 50.49% of reference with a coverageData >= 9X There is a 47.06% of reference with a coverageData >= 10X There is a 43.88% of reference with a coverageData >= 11X There is a 40.93% of reference with a coverageData >= 12X There is a 38.2% of reference with a coverageData >= 13X There is a 35.66% of reference with a coverageData >= 14X There is a 33.3% of reference with a coverageData >= 15X There is a 31.11% of reference with a coverageData >= 16X There is a 29.06% of reference with a coverageData >= 17X There is a 27.16% of reference with a coverageData >= 18X There is a 25.38% of reference with a coverageData >= 19X There is a 23.72% of reference with a coverageData >= 20X There is a 22.18% of reference with a coverageData >= 21X There is a 20.74% of reference with a coverageData >= 22X There is a 19.39% of reference with a coverageData >= 23X There is a 18.14% of reference with a coverageData >= 24X There is a 16.97% of reference with a coverageData >= 25X There is a 15.88% of reference with a coverageData >= 26X There is a 14.86% of reference with a coverageData >= 27X There is a 13.91% of reference with a coverageData >= 28X There is a 13.02% of reference with a coverageData >= 29X There is a 12.2% of reference with a coverageData >= 30X There is a 11.43% of reference with a coverageData >= 31X There is a 10.71% of reference with a coverageData >= 32X There is a 10.04% of reference with a coverageData >= 33X There is a 9.41% of reference with a coverageData >= 34X There is a 8.83% of reference with a coverageData >= 35X There is a 8.28% of reference with a coverageData >= 36X There is a 7.77% of reference with a coverageData >= 37X There is a 7.3% of reference with a coverageData >= 38X There is a 6.85% of reference with a coverageData >= 39X There is a 6.44% of reference with a coverageData >= 40X There is a 6.05% of reference with a coverageData >= 41X There is a 5.69% of reference with a coverageData >= 42X There is a 5.36% of reference with a coverageData >= 43X There is a 5.04% of reference with a coverageData >= 44X There is a 4.75% of reference with a coverageData >= 45X There is a 4.48% of reference with a coverageData >= 46X There is a 4.22% of reference with a coverageData >= 47X There is a 3.98% of reference with a coverageData >= 48X There is a 3.76% of reference with a coverageData >= 49X There is a 3.55% of reference with a coverageData >= 50X There is a 3.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3426367585 13.74667622192203 111.09322932214863 chr2 243199373 3664985279 15.069879637395282 340.6215023208894 chr3 198022430 2506071598 12.655493612516521 38.6571682855679 chr4 191154276 3513778042 18.381896107832816 840.466712815665 chr5 180915260 3012445590 16.65114147916544 47.4273792928081 chr6 171115067 1450550223 8.477045583601356 34.48616992669436 chr7 159138663 2284735538 14.356885340930633 53.59143935987589 chr8 146364022 2706389363 18.490810282598 252.09404603683632 chr9 141213431 1271727445 9.00571168049872 159.70057846231384 chr10 135534747 3618988671 26.701556251106588 814.4388188314116 chr11 135006516 1971299421 14.601513166964475 39.22528605477334 chr12 133851895 1839014315 13.739172799906942 34.266204078423286 chr13 115169878 756671396 6.5700459976175365 16.54759060390604 chr14 107349540 1249616741 11.640634333412141 40.71855980409046 chr15 102531392 1653667300 16.1283999733467 26.97316744405642 chr16 90354753 2556975912 28.299296131106683 332.8318448990305 chr17 81195210 1540690099 18.975135343575072 107.42414789986715 chr18 78077248 805585354 10.3177990341053 420.36028018497905 chr19 59128983 1841894857 31.15045724699848 67.39965292881035 chr20 63025520 1415630767 22.4612310537065 229.43157205893723 chr21 48129895 921168869 19.139224571339703 303.6227129275034 chr22 51304566 839213214 16.35747613574979 43.66964121883718 chrMT 16571 16227398 979.2648602981111 455.24076288468734 chrX 155270560 2823346357 18.18339778641875 36.95389005574842 chrY 59373566 795180800 13.392842195127711 781.3129396077541