BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094131.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 = 430,312 number of mapped reads = 403,445 (93.76%) number of supplementary alignments = 3,724 (0.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,394 number of mapped paired reads (second in pair) = 201,051 number of mapped paired reads (both in pair) = 401,204 number of mapped paired reads (singletons) = 2,241 number of mapped bases = 58,159,077 bp number of sequenced bases = 57,853,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 400,587 duplication rate = 46.64% >>>>>>> Insert size mean insert size = 17,854.7943 std insert size = 1,345,050.243 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 26.8698 >>>>>>> ACTG content number of A's = 15,806,656 bp (27.32%) number of C's = 12,443,383 bp (21.51%) number of T's = 16,484,895 bp (28.49%) number of G's = 13,117,555 bp (22.67%) number of N's = 692 bp (0%) GC percentage = 44.18% >>>>>>> Mismatches and indels general error rate = 0.0204 number of mismatches = 1,155,988 number of insertions = 22,546 mapped reads with insertion percentage = 5.51% number of deletions = 68,428 mapped reads with deletion percentage = 16.56% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 25.9402X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 174609 7.005358674713191E-4 0.5780621613789731 chr2 243199373 329003 0.0013528118758760123 0.9823651140776954 chr3 198022430 358857 0.001812203799337277 1.111638129934316 chr4 191154276 43195 2.2596931077806495E-4 0.21008415519401658 chr5 180915260 74855 4.1375724745386323E-4 0.31546008634347694 chr6 171115067 86807 5.073019081364706E-4 0.26133517533494444 chr7 159138663 379749 0.0023862774315252353 2.1770194655672617 chr8 146364022 16995 1.1611460089556708E-4 0.04207126353009268 chr9 141213431 537824 0.0038085895668096897 2.898397545054892 chr10 135534747 259700 0.0019161138065945554 1.528981446746427 chr11 135006516 1044846 0.007739226453336519 6.059616604631906 chr12 133851895 179049 0.001337665036419544 0.7913197337138501 chr13 115169878 1201362 0.010431217093066644 8.735536033081672 chr14 107349540 3650125 0.03400224164910255 25.903764041050525 chr15 102531392 253295 0.0024704141342390047 1.1915488696435825 chr16 90354753 13431 1.48647409837975E-4 0.08156245294024692 chr17 81195210 7150 8.805938182806597E-5 0.017029665583063434 chr18 78077248 167492 0.0021452088065399026 1.2403244090078929 chr19 59128983 6958 1.1767494800307998E-4 0.061391500320007446 chr20 63025520 35257 5.594083158695081E-4 0.21302878489474758 chr21 48129895 1907 3.962194390825079E-5 0.007386417400477794 chr22 51304566 65923 0.0012849343662706357 0.4695035088810203 chrMT 16571 42473168 2563.102287128115 10543.835879630835 chrX 155270560 6790893 0.043735869826192424 16.66970754008478 chrY 59373566 6627 1.1161532726533555E-4 0.028863514600536554