BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617657.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 = 30,218,467 (94.43%) number of supplementary alignments = 170,795 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,292,901 number of mapped paired reads (second in pair) = 14,925,566 number of mapped paired reads (both in pair) = 29,488,294 number of mapped paired reads (singletons) = 730,173 number of mapped bases = 2,921,076,951 bp number of sequenced bases = 2,919,291,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,920,180 duplication rate = 10.66% >>>>>>> Insert size mean insert size = 43,077.7561 std insert size = 1,916,090.6448 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.5649 >>>>>>> ACTG content number of A's = 869,790,303 bp (29.79%) number of C's = 580,980,521 bp (19.9%) number of T's = 868,448,819 bp (29.75%) number of G's = 596,576,697 bp (20.44%) number of N's = 3,494,798 bp (0.12%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 40,314,669 number of insertions = 459,799 mapped reads with insertion percentage = 1.49% number of deletions = 1,072,265 mapped reads with deletion percentage = 3.47% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.9436X std coverageData = 10.6497X There is a 33.19% of reference with a coverageData >= 1X There is a 19.19% of reference with a coverageData >= 2X There is a 11.71% of reference with a coverageData >= 3X There is a 7.47% of reference with a coverageData >= 4X There is a 4.91% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.18% 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 0.5% 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 178991209 0.7181174044095963 10.179623274612837 chr2 243199373 301489774 1.239681543093452 12.22212329660763 chr3 198022430 244337661 1.233888812494625 2.478873926659021 chr4 191154276 163281880 0.8541890007210721 8.461139616300882 chr5 180915260 193493245 1.0695241794418004 2.318356463571983 chr6 171115067 141454468 0.8266628443654234 5.716135475940489 chr7 159138663 228691717 1.4370594341363796 13.379093817494851 chr8 146364022 129785646 0.8867318909834276 4.127394552366556 chr9 141213431 119918513 0.8492004772548866 20.574927879067022 chr10 135534747 123773310 0.9132219798956794 21.641515120801053 chr11 135006516 160749068 1.1906763670577203 12.11678779153983 chr12 133851895 124637986 0.9311634026548522 2.164025474714353 chr13 115169878 125391885 1.08875590716524 2.3010047713760424 chr14 107349540 83439593 0.777270149457557 2.466798513659752 chr15 102531392 62482971 0.6094033230330083 1.6670262102988491 chr16 90354753 81087675 0.897436740267554 16.73935536200568 chr17 81195210 72143849 0.8885234609282986 12.786687675847622 chr18 78077248 53987977 0.6914687490009894 18.470298732390134 chr19 59128983 31162963 0.5270336376324958 6.102162097103053 chr20 63025520 78934106 1.252414989991356 3.059845046593388 chr21 48129895 42597415 0.8850510685718305 4.333433635701929 chr22 51304566 18858546 0.36758026566290414 1.2760807566794996 chrMT 16571 3076658 185.66519823788545 129.7245902948 chrX 155270560 145414420 0.9365228025196792 4.344033529215971 chrY 59373566 11894416 0.2003318446461511 17.53966077213868