BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093982.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 366,446 number of mapped reads = 352,425 (96.17%) number of supplementary alignments = 22,058 (6.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,194 number of mapped paired reads (second in pair) = 175,231 number of mapped paired reads (both in pair) = 349,158 number of mapped paired reads (singletons) = 3,267 number of mapped bases = 45,187,985 bp number of sequenced bases = 44,384,591 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,070 duplication rate = 50.21% >>>>>>> Insert size mean insert size = 1,094,611.6285 std insert size = 9,538,011.294 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.818 >>>>>>> ACTG content number of A's = 11,699,594 bp (26.36%) number of C's = 10,444,154 bp (23.53%) number of T's = 11,062,229 bp (24.92%) number of G's = 11,178,009 bp (25.18%) number of N's = 605 bp (0%) GC percentage = 48.72% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 1,515,210 number of insertions = 24,386 mapped reads with insertion percentage = 6.79% number of deletions = 118,623 mapped reads with deletion percentage = 32.31% homopolymer indels = 28.9% >>>>>>> Coverage mean coverageData = 0.0146X std coverageData = 2.9512X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 742939 0.0029806906679682855 1.0676779404530479 chr2 243199373 2268198 0.009326496084346401 2.9272624130583 chr3 198022430 699945 0.003534675339556231 1.2445257255708138 chr4 191154276 1207696 0.0063179125535229985 2.1936195869636355 chr5 180915260 523358 0.0028928350212137992 1.3381068237097513 chr6 171115067 905703 0.005292947113768771 1.5106640662880835 chr7 159138663 833487 0.0052374890192460645 1.723380698812605 chr8 146364022 556392 0.003801426008913584 1.1659639021400832 chr9 141213431 510255 0.003613360261744508 1.0362073899282755 chr10 135534747 702653 0.005184301557740024 1.5962608193578183 chr11 135006516 1093666 0.008100838629151796 2.026156197568353 chr12 133851895 996178 0.007442389963922438 1.8060886018436857 chr13 115169878 970479 0.008426500199991529 2.283656457024374 chr14 107349540 174490 0.0016254377988019326 0.5443327088304024 chr15 102531392 558907 0.005451081752601194 1.6237049824199954 chr16 90354753 259586 0.0028729645246221855 0.7213769291188687 chr17 81195210 1050506 0.012938029226108289 3.2834047968649664 chr18 78077248 241902 0.00309823932318926 0.9340331671868113 chr19 59128983 134913 0.0022816729318682854 0.51335924609192 chr20 63025520 219108 0.0034764965049078533 1.0615764668828247 chr21 48129895 107286 0.002229092749942629 0.4007546309133163 chr22 51304566 138639 0.0027022741016852186 0.8729433686300402 chrMT 16571 1127676 68.05117373725183 297.23615679224133 chrX 155270560 28453033 0.18324808643699103 10.37572474051304 chrY 59373566 710990 0.011974857632772134 1.864261120546873