BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708522.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 = 3,302,302 number of mapped reads = 2,280,402 (69.05%) number of supplementary alignments = 499 (0.02%) number of secondary alignments = 0 number of mapped bases = 109,509,522 bp number of sequenced bases = 109,489,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,350 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.081 >>>>>>> ACTG content number of A's = 31,893,841 bp (29.13%) number of C's = 20,186,775 bp (18.44%) number of T's = 35,183,928 bp (32.13%) number of G's = 22,223,333 bp (20.3%) number of N's = 1,645 bp (0%) GC percentage = 38.73% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 530,158 number of insertions = 5,252 mapped reads with insertion percentage = 0.23% number of deletions = 13,116 mapped reads with deletion percentage = 0.57% homopolymer indels = 48.75% >>>>>>> Coverage mean coverageData = 0.0354X std coverageData = 0.3763X There is a 3.02% of reference with a coverageData >= 1X There is a 0.38% 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 8584390 0.03444079683957939 0.737307180562556 chr2 243199373 9380471 0.03857111506615603 0.3048188985603954 chr3 198022430 7723370 0.039002500878309594 0.22739876106937598 chr4 191154276 7677829 0.04016561471007847 0.23508490044470517 chr5 180915260 7230532 0.0399664019497305 0.23240451135760404 chr6 171115067 6806552 0.039777631037014406 0.28115834220695174 chr7 159138663 6392764 0.04017102996523227 0.47595978639607356 chr8 146364022 5934271 0.04054460186944029 0.7666853325291222 chr9 141213431 4699187 0.033277195849734716 0.2571104349742605 chr10 135534747 5144766 0.03795901873045146 0.2925993436436021 chr11 135006516 5097605 0.03775821457388027 0.3311847632573338 chr12 133851895 5082024 0.03796751626116313 0.22650076479009337 chr13 115169878 3848174 0.03341302488833061 0.20960232256725705 chr14 107349540 3352500 0.03122975655042397 0.21034507117088644 chr15 102531392 3071234 0.02995408469632403 0.19675262794380236 chr16 90354753 2837503 0.03140402586236941 0.21149919551423235 chr17 81195210 2597966 0.03199654265319346 0.2693109034678903 chr18 78077248 3061551 0.039211820068248304 0.4406360193575903 chr19 59128983 1817157 0.030732086158153607 0.5104587492476137 chr20 63025520 2125779 0.03372886094394779 0.2110631018419366 chr21 48129895 1497310 0.0311097707568238 0.24414050360446046 chr22 51304566 1032837 0.020131483034083165 0.17631486595511953 chrMT 16571 166663 10.057510108020034 7.107391211929898 chrX 155270560 3555327 0.02289762463663427 0.19838074616512802 chrY 59373566 791760 0.013335227329953535 0.1461825376411483