BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094053.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 = 383,550 number of mapped reads = 352,712 (91.96%) number of supplementary alignments = 11,471 (2.99%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,131 number of mapped paired reads (second in pair) = 175,581 number of mapped paired reads (both in pair) = 349,856 number of mapped paired reads (singletons) = 2,856 number of mapped bases = 46,112,033 bp number of sequenced bases = 44,871,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 329,261 duplication rate = 49.92% >>>>>>> Insert size mean insert size = 488,176.9365 std insert size = 6,255,494.56 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 43.7028 >>>>>>> ACTG content number of A's = 12,431,036 bp (27.7%) number of C's = 10,013,138 bp (22.32%) number of T's = 11,963,090 bp (26.66%) number of G's = 10,463,619 bp (23.32%) number of N's = 674 bp (0%) GC percentage = 45.63% >>>>>>> Mismatches and indels general error rate = 0.0463 number of mismatches = 2,027,640 number of insertions = 32,645 mapped reads with insertion percentage = 9.05% number of deletions = 163,067 mapped reads with deletion percentage = 42.89% homopolymer indels = 29.84% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 3.2963X 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% 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 843583 0.003384477024031166 1.1621763903698312 chr2 243199373 1646915 0.0067718718995217145 2.2116602304600064 chr3 198022430 1409750 0.007119143018293432 2.0746846479831897 chr4 191154276 920918 0.0048176688446142845 2.269671097147079 chr5 180915260 349097 0.0019296161086687768 0.7075620966032857 chr6 171115067 1371732 0.008016430253917968 3.4802523385193904 chr7 159138663 1378280 0.008660874573264449 2.6596909428834046 chr8 146364022 999872 0.0068314056032157955 2.346422468936377 chr9 141213431 548893 0.0038869744620821513 1.6350389530690452 chr10 135534747 1088456 0.008030826220526312 2.440451323909826 chr11 135006516 1730662 0.01281909978330231 3.1209647614434095 chr12 133851895 1394423 0.010417656021978621 2.697787767790287 chr13 115169878 1317774 0.011442002222143536 3.011692697863903 chr14 107349540 242156 0.002255771193802973 0.935739809137106 chr15 102531392 457056 0.004457717690987751 1.715416602081957 chr16 90354753 274252 0.0030352802801641215 0.8142373208039771 chr17 81195210 739243 0.009104514909192304 2.639316717797869 chr18 78077248 142969 0.001831122428905281 0.5200149786481569 chr19 59128983 140879 0.002382570997373657 0.49070656399512247 chr20 63025520 197342 0.003131144336452916 0.7718582356555963 chr21 48129895 327512 0.006804752015353451 2.2394552587299725 chr22 51304566 116507 0.0022708894954885693 0.8870416265198615 chrMT 16571 2057520 124.16390079053768 518.430775387545 chrX 155270560 26125441 0.16825753059691417 9.970327359058558 chrY 59373566 290801 0.004897819342702104 1.5197186405067489