BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124896.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,093,936 number of mapped reads = 4,020,590 (98.21%) number of supplementary alignments = 18,695 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,014,712 number of mapped paired reads (second in pair) = 2,005,878 number of mapped paired reads (both in pair) = 4,003,460 number of mapped paired reads (singletons) = 17,130 number of mapped bases = 347,362,234 bp number of sequenced bases = 347,145,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,196 duplication rate = 5.78% >>>>>>> Insert size mean insert size = 34,744.3866 std insert size = 1,751,640.5093 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.6629 >>>>>>> ACTG content number of A's = 97,160,181 bp (27.99%) number of C's = 64,737,872 bp (18.65%) number of T's = 103,134,411 bp (29.71%) number of G's = 81,981,692 bp (23.62%) number of N's = 130,926 bp (0.04%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,664,141 number of insertions = 51,766 mapped reads with insertion percentage = 1.25% number of deletions = 124,436 mapped reads with deletion percentage = 3.03% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.1122X std coverageData = 0.9378X There is a 7.81% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 25866474 0.10377696912538485 1.0002890147006354 chr2 243199373 32513989 0.13369273365684212 1.4823574629695087 chr3 198022430 25400143 0.12826901982770336 0.46701195172133136 chr4 191154276 19151130 0.10018677269871797 0.7268308478424365 chr5 180915260 18019075 0.09959953074163008 0.43528604825351475 chr6 171115067 20123249 0.11760068445638396 0.7851412012261901 chr7 159138663 19259944 0.12102617702650927 1.1607711807479104 chr8 146364022 25672427 0.17540121301121392 0.817226482664108 chr9 141213431 14237006 0.10081906444154026 1.2942915251762324 chr10 135534747 16727691 0.12341994485000957 1.4639236422042476 chr11 135006516 13499256 0.09998966272116822 0.8853911167042051 chr12 133851895 21636692 0.16164651236353433 0.551445923007919 chr13 115169878 6801952 0.0590601650198848 0.311287397836067 chr14 107349540 8930015 0.08318633689534208 0.4087737060538391 chr15 102531392 6282053 0.061269557327379306 0.318225856238948 chr16 90354753 9470543 0.10481510585281552 0.9491902458197569 chr17 81195210 12502187 0.15397690331732622 1.611939899688525 chr18 78077248 7167299 0.0917975362041449 1.1996034289277702 chr19 59128983 6619512 0.11195037804049496 0.6317227435277636 chr20 63025520 6977869 0.11071497704421955 0.4925118727508865 chr21 48129895 4424159 0.09192122692143832 0.5211610530108434 chr22 51304566 4221012 0.08227361283983964 0.4063798669537147 chrMT 16571 578523 34.911773580351216 22.288439918891385 chrX 155270560 20284441 0.13063932402897238 0.5927847053176032 chrY 59373566 995593 0.016768287085872524 1.1518647371194362