BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617662.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,238,921 (94.5%) number of supplementary alignments = 143,054 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,139,367 number of mapped paired reads (second in pair) = 15,099,554 number of mapped paired reads (both in pair) = 29,643,580 number of mapped paired reads (singletons) = 595,341 number of mapped bases = 2,937,154,765 bp number of sequenced bases = 2,935,371,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,915,058 duplication rate = 10.66% >>>>>>> Insert size mean insert size = 32,683.971 std insert size = 1,660,676.0999 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 52.6514 >>>>>>> ACTG content number of A's = 875,064,921 bp (29.81%) number of C's = 584,802,272 bp (19.92%) number of T's = 872,793,318 bp (29.73%) number of G's = 600,746,060 bp (20.47%) number of N's = 1,965,325 bp (0.07%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 44,064,929 number of insertions = 455,115 mapped reads with insertion percentage = 1.48% number of deletions = 1,076,280 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.9488X std coverageData = 10.727X There is a 33.3% of reference with a coverageData >= 1X There is a 19.29% of reference with a coverageData >= 2X There is a 11.79% of reference with a coverageData >= 3X There is a 7.53% of reference with a coverageData >= 4X There is a 4.95% of reference with a coverageData >= 5X There is a 3.36% of reference with a coverageData >= 6X There is a 2.33% of reference with a coverageData >= 7X There is a 1.65% of reference with a coverageData >= 8X There is a 1.2% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179755160 0.7211823957702396 10.535315357901126 chr2 243199373 303153153 1.2465211125359275 12.27307706005301 chr3 198022430 246285646 1.2437260061903088 2.482455398945679 chr4 191154276 164678956 0.8614976313687066 8.324850316878807 chr5 180915260 194387582 1.0744675822260654 2.33721337424399 chr6 171115067 142667177 0.8337499409096453 5.8519185862164855 chr7 159138663 229607229 1.4428123541543139 13.339103298618614 chr8 146364022 130581933 0.8921723468353445 4.120049753336078 chr9 141213431 120791843 0.8553849456430246 20.94909643744946 chr10 135534747 124417819 0.9179772844523774 21.709272738824087 chr11 135006516 161726576 1.1979168175853083 12.09358887888802 chr12 133851895 125603702 0.9383782127253409 2.1718960025739276 chr13 115169878 126114115 1.0950269045175163 2.283171246523096 chr14 107349540 84093432 0.7833608974942976 2.463298515857518 chr15 102531392 62595820 0.610503951804341 1.571936728203276 chr16 90354753 81198209 0.8986600738092881 16.998339989618234 chr17 81195210 72259995 0.8899539147691101 12.829545716302652 chr18 78077248 54302025 0.6954910219171659 18.411094698238863 chr19 59128983 31002466 0.5243192834891139 6.133002458827129 chr20 63025520 79163040 1.256047391596293 3.028954853424508 chr21 48129895 42819470 0.8896647291667684 4.37188897420389 chr22 51304566 18853474 0.3674814050663639 1.2638068754192973 chrMT 16571 3054479 184.3267756924748 126.75271793544678 chrX 155270560 146200617 0.9415862028191306 4.390141037973118 chrY 59373566 11840847 0.19942960811887228 17.56498687993242