BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081117.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,496,705 number of mapped reads = 2,315,270 (92.73%) number of supplementary alignments = 13,835 (0.55%) number of secondary alignments = 0 number of mapped bases = 159,300,838 bp number of sequenced bases = 159,239,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,086 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8884 >>>>>>> ACTG content number of A's = 45,830,371 bp (28.78%) number of C's = 29,887,817 bp (18.77%) number of T's = 49,828,124 bp (31.29%) number of G's = 33,691,636 bp (21.16%) number of N's = 1,803 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,401,026 number of insertions = 12,479 mapped reads with insertion percentage = 0.53% number of deletions = 34,239 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0515X std coverageData = 0.6212X There is a 4.21% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13008662 0.05219109163222506 1.008050731140485 chr2 243199373 11070137 0.045518772780717656 0.6825163295718426 chr3 198022430 14027042 0.07083562200504256 0.31597192713487343 chr4 191154276 10669299 0.05581512076664191 0.32180578334135596 chr5 180915260 9311019 0.051466189198191466 0.2733229888653682 chr6 171115067 13417560 0.07841249888298849 0.6369047520491996 chr7 159138663 8352122 0.05248329879458646 0.864617849862623 chr8 146364022 12748741 0.08710296988149178 0.6849700075374434 chr9 141213431 8074389 0.05717861922071704 0.8188316735966801 chr10 135534747 7025928 0.05183857391197255 0.5164140543953145 chr11 135006516 6942852 0.05142605116926356 0.5112143096455901 chr12 133851895 7876056 0.05884157262024568 0.33966731750219575 chr13 115169878 4135636 0.035909007388199195 0.21680926044864474 chr14 107349540 4490264 0.04182844192904785 0.45480200737565274 chr15 102531392 3728682 0.03636624771465114 0.22955597635688701 chr16 90354753 3664372 0.04055538727442484 0.4257982967667465 chr17 81195210 2847971 0.03507560359779844 0.2596612880741124 chr18 78077248 4389082 0.0562146094083644 1.659429683018184 chr19 59128983 2109559 0.03567724139615255 0.7419869510067179 chr20 63025520 2247248 0.03565615960011119 0.28523870236456156 chr21 48129895 2767527 0.057501205851373666 0.433075296665909 chr22 51304566 998483 0.019461874017217103 0.1593710368363599 chrMT 16571 127052 7.66712932231006 4.572307413859344 chrX 155270560 4874851 0.03139584863994823 0.3030963319746038 chrY 59373566 396304 0.006674754890080208 0.19286503303058583