BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094157.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 14,678 number of mapped reads = 670 (4.56%) number of supplementary alignments = 25 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 269 number of mapped paired reads (second in pair) = 401 number of mapped paired reads (both in pair) = 462 number of mapped paired reads (singletons) = 208 number of mapped bases = 64,464 bp number of sequenced bases = 64,301 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 456 duplication rate = 18.41% >>>>>>> Insert size mean insert size = 119.2545 std insert size = 69.7122 median insert size = 114 >>>>>>> Mapping quality mean mapping quality = 6.501 >>>>>>> ACTG content number of A's = 10,124 bp (15.74%) number of C's = 8,361 bp (13%) number of T's = 8,942 bp (13.91%) number of G's = 36,874 bp (57.35%) number of N's = 0 bp (0%) GC percentage = 70.35% >>>>>>> Mismatches and indels general error rate = 0.0239 number of mismatches = 1,310 number of insertions = 38 mapped reads with insertion percentage = 4.63% number of deletions = 35 mapped reads with deletion percentage = 5.07% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0433X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 204 8.184533269427642E-7 0.0015873095881906204 chr2 243199373 28813 1.1847481202182212E-4 0.12608728713125159 chr3 198022430 846 4.272243300923032E-6 0.0024942934436741355 chr4 191154276 173 9.050281459568291E-7 9.513292421033237E-4 chr5 180915260 846 4.676222448012401E-6 0.0027618579698515233 chr6 171115067 774 4.5232720506137546E-6 0.002446274059652859 chr7 159138663 137 8.608844476719023E-7 0.0011126155632839457 chr8 146364022 745 5.090048700629448E-6 0.0027847107555729984 chr9 141213431 66 4.6737763917088027E-7 6.836500718415985E-4 chr10 135534747 471 3.475123615348616E-6 0.002492472071686438 chr11 135006516 1008 7.466306292949594E-6 0.004300621809656547 chr12 133851895 916 6.843384622981991E-6 0.0032708324398278074 chr13 115169878 565 4.9057966354709515E-6 0.002986174498592132 chr14 107349540 585 5.44948772020821E-6 0.003019886040461256 chr15 102531392 57 5.559273007821839E-7 7.45605117825126E-4 chr16 90354753 435 4.814356583986235E-6 0.002625837171103907 chr17 81195210 762 9.384790063354722E-6 0.003948666310642602 chr18 78077248 71 9.093558215576451E-7 9.536010668144383E-4 chr19 59128983 42 7.103115573626558E-7 8.427995329971103E-4 chr20 63025520 17244 2.7360345460061255E-4 0.17088193653967929 chr21 48129895 0 0.0 0.0 chr22 51304566 0 0.0 0.0 chrMT 16571 601 0.03626817934946593 0.22955312384528243 chrX 155270560 8778 5.653357597216111E-5 0.022361000668384173 chrY 59373566 325 5.47381641183553E-6 0.0031496364862559595