BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708523.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,471,990 number of mapped reads = 2,424,995 (69.84%) number of supplementary alignments = 520 (0.01%) number of secondary alignments = 0 number of mapped bases = 116,663,130 bp number of sequenced bases = 116,642,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,259 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1933 >>>>>>> ACTG content number of A's = 34,063,267 bp (29.2%) number of C's = 21,532,025 bp (18.46%) number of T's = 37,380,307 bp (32.05%) number of G's = 23,665,148 bp (20.29%) number of N's = 1,690 bp (0%) GC percentage = 38.75% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 566,473 number of insertions = 5,562 mapped reads with insertion percentage = 0.23% number of deletions = 13,921 mapped reads with deletion percentage = 0.57% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3917X There is a 3.21% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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% 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 9375319 0.03761402464068485 0.7592536537239689 chr2 243199373 10182884 0.041870519131642664 0.3246294370888856 chr3 198022430 8281168 0.04181934339458414 0.23564253891403278 chr4 191154276 8214554 0.042973425297585285 0.24268191823913757 chr5 180915260 7564905 0.04181463188898493 0.23669049986319315 chr6 171115067 7270664 0.04248991118941034 0.29272277072217107 chr7 159138663 6758540 0.042469503466923055 0.5024142420997773 chr8 146364022 6291933 0.042988248847110805 0.8096231872433883 chr9 141213431 4896847 0.03467692106425769 0.26571058309936363 chr10 135534747 5438333 0.040125009419171305 0.3099233527729 chr11 135006516 5368199 0.03976251783284297 0.3232476576074635 chr12 133851895 5297955 0.03958072465092855 0.23452349783009513 chr13 115169878 4092383 0.03553344911939561 0.21812746188512977 chr14 107349540 3643501 0.03394053668045527 0.21758888638217 chr15 102531392 3239676 0.03159691814190916 0.2022110419751426 chr16 90354753 2965516 0.032820807998888556 0.21730885963785046 chr17 81195210 2816439 0.03468725556593794 0.27340321033099524 chr18 78077248 3274361 0.04193745404551144 0.46880666924797426 chr19 59128983 1941626 0.03283712828275771 0.5246648327180256 chr20 63025520 2283735 0.036235083820014495 0.21900879722081615 chr21 48129895 1548957 0.032182846025323765 0.25669084716899604 chr22 51304566 1091987 0.021284401860060566 0.18995882054839633 chrMT 16571 203392 12.273972602739725 8.000017153235811 chrX 155270560 3772597 0.02429692402732366 0.20461872477662127 chrY 59373566 847659 0.01427670691027721 0.15185149525371425