BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777279.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 12,196,784 number of mapped reads = 11,398,263 (93.45%) number of supplementary alignments = 1,131,204 (9.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,718,269 number of mapped paired reads (second in pair) = 5,679,994 number of mapped paired reads (both in pair) = 11,151,474 number of mapped paired reads (singletons) = 246,789 number of mapped bases = 1,032,156,461 bp number of sequenced bases = 1,027,806,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,366,697 duplication rate = 8.34% >>>>>>> Insert size mean insert size = 621,278.6413 std insert size = 7,522,458.1698 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 49.0084 >>>>>>> ACTG content number of A's = 295,894,516 bp (28.79%) number of C's = 219,473,658 bp (21.35%) number of T's = 289,759,734 bp (28.19%) number of G's = 222,660,215 bp (21.66%) number of N's = 18,225 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0188 number of mismatches = 15,547,444 number of insertions = 1,121,128 mapped reads with insertion percentage = 8.58% number of deletions = 1,118,654 mapped reads with deletion percentage = 8.62% homopolymer indels = 21.53% >>>>>>> Coverage mean coverageData = 0.3334X std coverageData = 49.9174X There is a 13.08% of reference with a coverageData >= 1X There is a 5.5% of reference with a coverageData >= 2X There is a 1.96% of reference with a coverageData >= 3X There is a 0.9% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 66386767 0.26634544272609856 14.30926924549447 chr2 243199373 142349423 0.5853198601790803 122.05404820857709 chr3 198022430 48360943 0.24421952099062716 5.932256971553609 chr4 191154276 61747503 0.32302444021707366 29.785652310294054 chr5 180915260 55822279 0.30855483943145534 19.857294069103485 chr6 171115067 50335175 0.2941598065119537 26.86320501588194 chr7 159138663 67277336 0.42275921345399264 34.38950520250881 chr8 146364022 39884351 0.2725010590375823 9.30112487143675 chr9 141213431 60283119 0.4268936642435945 41.33808650969902 chr10 135534747 56745081 0.4186755223736095 110.03799598206275 chr11 135006516 48217896 0.35715236144602086 14.880506944780372 chr12 133851895 39397120 0.29433367379669895 7.236189002402982 chr13 115169878 41105534 0.3569121953919236 19.779949454695384 chr14 107349540 16639041 0.15499871727442893 21.065203923294046 chr15 102531392 29231526 0.285098304332004 7.714511538193006 chr16 90354753 47199199 0.5223764930219 77.55259783372976 chr17 81195210 21401738 0.2635837508148572 7.612471216171751 chr18 78077248 19636275 0.2514980420416457 18.18878342371233 chr19 59128983 22473008 0.380067555026272 24.013768997829228 chr20 63025520 21418012 0.33983078600541494 13.751380377442151 chr21 48129895 6845504 0.14222977216135627 3.8234724532973154 chr22 51304566 8967049 0.174780720296903 13.664114505724584 chrMT 16571 4714304 284.4912196005069 49.686698936732405 chrX 155270560 33951739 0.2186617926798229 15.76074644791782 chrY 59373566 21766539 0.36660319509864037 114.54910010378552