BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 18,200,026 number of mapped reads = 17,895,373 (98.33%) number of supplementary alignments = 119,314 (0.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,988,094 number of mapped paired reads (second in pair) = 8,907,279 number of mapped paired reads (both in pair) = 17,725,428 number of mapped paired reads (singletons) = 169,945 number of mapped bases = 1,705,241,914 bp number of sequenced bases = 1,703,958,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 895,872 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 73,513.317 std insert size = 2,669,086.3539 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.635 >>>>>>> ACTG content number of A's = 496,467,847 bp (29.14%) number of C's = 336,591,914 bp (19.75%) number of T's = 501,407,983 bp (29.43%) number of G's = 369,211,326 bp (21.67%) number of N's = 279,134 bp (0.02%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 18,404,199 number of insertions = 276,986 mapped reads with insertion percentage = 1.52% number of deletions = 923,221 mapped reads with deletion percentage = 5.02% homopolymer indels = 53.16% >>>>>>> Coverage mean coverageData = 0.5508X std coverageData = 2.1974X There is a 26.15% of reference with a coverageData >= 1X There is a 12.98% of reference with a coverageData >= 2X There is a 6.58% of reference with a coverageData >= 3X There is a 3.59% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.16% of reference with a coverageData >= 6X There is a 0.69% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 140091182 0.562049480310021 2.493034934856119 chr2 243199373 153344235 0.6305289076547085 3.739696906674758 chr3 198022430 120255538 0.6072824073515308 1.3057339123002 chr4 191154276 103570515 0.5418163651227975 1.6292270006341207 chr5 180915260 105401028 0.5825988808240941 1.2610835735845782 chr6 171115067 100053081 0.58471228018746 1.2771470931838245 chr7 159138663 86939153 0.546310691324584 1.6290080528173159 chr8 146364022 86616591 0.5917888140570502 1.5224472039355408 chr9 141213431 73973158 0.5238393931523412 3.1713505022888286 chr10 135534747 82857744 0.611339496579427 4.229343117825338 chr11 135006516 78910742 0.584495803150716 2.2215541468509827 chr12 133851895 76452682 0.5711736991097511 1.2677892525110288 chr13 115169878 53672443 0.4660284783839052 1.1280991746724045 chr14 107349540 51241649 0.4773345931431099 1.1984778609736069 chr15 102531392 51523591 0.5025152784427231 1.227010061820283 chr16 90354753 50464384 0.5585138836027806 2.9289445919362516 chr17 81195210 40534640 0.49922452322002736 1.528287149073155 chr18 78077248 45834414 0.5870393126561018 3.1708373977772406 chr19 59128983 23430193 0.3962556399794666 1.5626255467208594 chr20 63025520 38598189 0.6124215873189146 1.4074685501345088 chr21 48129895 21472924 0.44614524922607873 1.4643659928339923 chr22 51304566 18872227 0.36784692808823294 1.079808730531327 chrMT 16571 56110 3.386035845754632 3.9941123347125638 chrX 155270560 98680675 0.6355401500451856 1.5327151029486659 chrY 59373566 2394826 0.04033488573012441 1.0866233457922672