BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549040.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,721,770 number of mapped reads = 7,999,235 (82.28%) number of secondary alignments = 0 number of mapped bases = 316,863,478 bp number of sequenced bases = 316,834,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 401,563 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7377 >>>>>>> ACTG content number of A's = 90,141,888 bp (28.45%) number of C's = 66,894,473 bp (21.11%) number of T's = 91,884,789 bp (29%) number of G's = 67,913,204 bp (21.43%) number of N's = 267 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 779,162 number of insertions = 8,788 mapped reads with insertion percentage = 0.11% number of deletions = 21,836 mapped reads with deletion percentage = 0.27% homopolymer indels = 42.23% >>>>>>> Coverage mean coverageData = 0.1024X std coverageData = 0.6372X There is a 7.15% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% 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% 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 23790983 0.09545004503719973 0.6855040650881076 chr2 243199373 26524763 0.1090659185210975 0.5586073561901964 chr3 198022430 22455689 0.11339972446555675 0.45794208390942903 chr4 191154276 21702784 0.11353543563943085 0.48109859524008347 chr5 180915260 23086736 0.12761077202663834 0.4860643139466546 chr6 171115067 19897061 0.11627883709387205 0.49736724308548314 chr7 159138663 16844034 0.10584501391720251 0.6423705945911937 chr8 146364022 16888884 0.11538958665675367 1.7451155798548283 chr9 141213431 13319638 0.09432274186440523 0.521133404626272 chr10 135534747 14409292 0.1063143756043607 0.539735864842895 chr11 135006516 13742869 0.10179411636694632 0.4678053756221504 chr12 133851895 15578910 0.11638916281312267 0.4714025057897475 chr13 115169878 9892073 0.0858911476835983 0.3990294460281822 chr14 107349540 9824211 0.0915160977867255 0.4705807534107279 chr15 102531392 9302035 0.0907237756023053 0.41542238366136464 chr16 90354753 8879293 0.09827145451883422 0.4490870696061492 chr17 81195210 8404164 0.10350566246457149 0.4427895330930999 chr18 78077248 8896676 0.11394710018467864 0.8026322366612024 chr19 59128983 5785757 0.09784976345694969 0.7144666516996956 chr20 63025520 6578499 0.10437833753692155 0.4618314275946637 chr21 48129895 4479503 0.09307111515618308 0.48856835644689517 chr22 51304566 3478675 0.06780439386233186 0.5081060570834799 chrMT 16571 36856 2.224126486029811 2.48828385831983 chrX 155270560 10563898 0.06803542152485313 0.38606680500003204 chrY 59373566 2500195 0.042109564380889634 0.3659695359041274