BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617365.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,640,623 (95.75%) number of supplementary alignments = 104,265 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,397,012 number of mapped paired reads (second in pair) = 15,243,611 number of mapped paired reads (both in pair) = 30,136,354 number of mapped paired reads (singletons) = 504,269 number of mapped bases = 3,006,698,522 bp number of sequenced bases = 3,005,787,651 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,642,251 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 73,737.946 std insert size = 2,607,406.3155 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 53.4348 >>>>>>> ACTG content number of A's = 908,086,515 bp (30.21%) number of C's = 598,042,282 bp (19.9%) number of T's = 897,927,041 bp (29.87%) number of G's = 600,423,490 bp (19.98%) number of N's = 1,308,323 bp (0.04%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 26,268,450 number of insertions = 310,493 mapped reads with insertion percentage = 0.98% number of deletions = 374,875 mapped reads with deletion percentage = 1.19% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.9713X std coverageData = 9.9255X There is a 53.67% of reference with a coverageData >= 1X There is a 24.35% of reference with a coverageData >= 2X There is a 9.37% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% 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 0.04% 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 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 195752650 0.7853647433841299 20.130183987542615 chr2 243199373 296680335 1.2199058383263184 9.031072167562401 chr3 198022430 238683610 1.205336233880172 1.5121882773654864 chr4 191154276 163997469 0.85793251624672 9.812765724085105 chr5 180915260 187594962 1.0369217168302995 1.4809990039128083 chr6 171115067 140636590 0.8218831483729017 3.635900373751957 chr7 159138663 243960651 1.5330067904365892 10.97399862007039 chr8 146364022 126372658 0.8634134008697848 7.823834010780794 chr9 141213431 126584549 0.8964058737444033 15.127321653931594 chr10 135534747 126560631 0.9337873408949514 20.19521200604507 chr11 135006516 161235229 1.1942773858411397 5.709635439271692 chr12 133851895 132677457 0.9912258395744042 1.4175746684346622 chr13 115169878 130426391 1.1324696462733077 1.35742321459233 chr14 107349540 87225128 0.8125337844950243 1.4031346463567673 chr15 102531392 67917603 0.6624078896734378 1.1810478221678453 chr16 90354753 75778836 0.8386812368354325 7.7832891786200475 chr17 81195210 94659578 1.165827122067915 7.217240846461278 chr18 78077248 54455104 0.6974516314919297 15.619384817228594 chr19 59128983 56729656 0.9594221500478031 9.689888470272184 chr20 63025520 86905295 1.3788905668687859 2.537654504903586 chr21 48129895 47700321 0.9910746948440258 3.2753200253585204 chr22 51304566 27066667 0.5275683844591922 0.9421976669749212 chrMT 16571 2124221 128.1890652344457 23.090486148694726 chrX 155270560 124515808 0.8019279894398526 3.057724283695522 chrY 59373566 10457123 0.17612421999379319 8.683477378392949