BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104294.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 873,135,994 number of mapped reads = 834,310,901 (95.55%) number of supplementary alignments = 741,329 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 428,031,485 number of mapped paired reads (second in pair) = 406,279,416 number of mapped paired reads (both in pair) = 810,588,086 number of mapped paired reads (singletons) = 23,722,815 number of mapped bases = 63,951,010,237 bp number of sequenced bases = 63,935,822,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 314,272,469 duplication rate = 32.94% >>>>>>> Insert size mean insert size = 13,861.4003 std insert size = 1,071,115.454 median insert size = 120 >>>>>>> Mapping quality mean mapping quality = 52.3098 >>>>>>> ACTG content number of A's = 18,858,013,311 bp (29.5%) number of C's = 13,269,650,619 bp (20.75%) number of T's = 19,073,802,560 bp (29.83%) number of G's = 12,722,027,469 bp (19.9%) number of N's = 12,328,502 bp (0.02%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 396,113,369 number of insertions = 6,055,480 mapped reads with insertion percentage = 0.72% number of deletions = 6,852,485 mapped reads with deletion percentage = 0.81% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 20.6581X std coverageData = 194.0521X There is a 91.68% of reference with a coverageData >= 1X There is a 91.54% of reference with a coverageData >= 2X There is a 91.27% of reference with a coverageData >= 3X There is a 90.89% of reference with a coverageData >= 4X There is a 90.3% of reference with a coverageData >= 5X There is a 89.49% of reference with a coverageData >= 6X There is a 88.4% of reference with a coverageData >= 7X There is a 87% of reference with a coverageData >= 8X There is a 85.27% of reference with a coverageData >= 9X There is a 83.22% of reference with a coverageData >= 10X There is a 80.83% of reference with a coverageData >= 11X There is a 78.13% of reference with a coverageData >= 12X There is a 75.13% of reference with a coverageData >= 13X There is a 71.88% of reference with a coverageData >= 14X There is a 68.4% of reference with a coverageData >= 15X There is a 64.75% of reference with a coverageData >= 16X There is a 60.97% of reference with a coverageData >= 17X There is a 57.1% of reference with a coverageData >= 18X There is a 53.19% of reference with a coverageData >= 19X There is a 49.3% of reference with a coverageData >= 20X There is a 45.45% of reference with a coverageData >= 21X There is a 41.7% of reference with a coverageData >= 22X There is a 38.07% of reference with a coverageData >= 23X There is a 34.58% of reference with a coverageData >= 24X There is a 31.28% of reference with a coverageData >= 25X There is a 28.16% of reference with a coverageData >= 26X There is a 25.25% of reference with a coverageData >= 27X There is a 22.54% of reference with a coverageData >= 28X There is a 20.05% of reference with a coverageData >= 29X There is a 17.77% of reference with a coverageData >= 30X There is a 15.7% of reference with a coverageData >= 31X There is a 13.82% of reference with a coverageData >= 32X There is a 12.13% of reference with a coverageData >= 33X There is a 10.63% of reference with a coverageData >= 34X There is a 9.28% of reference with a coverageData >= 35X There is a 8.09% of reference with a coverageData >= 36X There is a 7.05% of reference with a coverageData >= 37X There is a 6.13% of reference with a coverageData >= 38X There is a 5.32% of reference with a coverageData >= 39X There is a 4.62% of reference with a coverageData >= 40X There is a 4% of reference with a coverageData >= 41X There is a 3.47% of reference with a coverageData >= 42X There is a 3.02% of reference with a coverageData >= 43X There is a 2.62% of reference with a coverageData >= 44X There is a 2.28% of reference with a coverageData >= 45X There is a 1.99% of reference with a coverageData >= 46X There is a 1.74% of reference with a coverageData >= 47X There is a 1.52% of reference with a coverageData >= 48X There is a 1.34% of reference with a coverageData >= 49X There is a 1.18% of reference with a coverageData >= 50X There is a 1.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4905508636 19.68102874255226 475.7339395486292 chr2 243199373 5705150880 23.45874008482744 114.99447859239861 chr3 198022430 4537661945 22.91488870730452 43.25183073715793 chr4 191154276 4903240496 25.65069742933713 82.86655299285414 chr5 180915260 4190675400 23.163747491505138 20.740241589974982 chr6 171115067 3971859887 23.21163154498838 68.42189610911716 chr7 159138663 3620440843 22.75022785003541 179.3366573204823 chr8 146364022 3451970204 23.584827451653386 306.40133218452894 chr9 141213431 2729418733 19.328322480883564 130.60120448404336 chr10 135534747 3112317427 22.96324371343682 355.12982534968563 chr11 135006516 2824271934 20.91952312879476 72.96888843668461 chr12 133851895 2808970273 20.98565935880101 22.72890303896745 chr13 115169878 2287661350 19.863365228189267 14.954845569274797 chr14 107349540 1872629441 17.444224176461304 27.75244314591047 chr15 102531392 1427374735 13.921343572512894 12.782453922664217 chr16 90354753 1618265181 17.91012788225983 135.85041110386078 chr17 81195210 1274868318 15.701274964372898 56.42409985166985 chr18 78077248 1796749930 23.012464911673117 183.65982550405352 chr19 59128983 887135554 15.00339611794101 322.88982047579003 chr20 63025520 1050733163 16.671550873360506 26.01227344441757 chr21 48129895 838804221 17.427925429714733 47.25125884929138 chr22 51304566 504507427 9.833577522125418 154.91350059409083 chrMT 16571 171391594 10342.863677508902 3884.121535631996 chrX 155270560 3288341012 21.17813584236445 41.609018024703516 chrY 59373566 171061653 2.8811079496218905 106.12456247426272