BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695968.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 409,059,110 number of mapped reads = 406,496,086 (99.37%) number of supplementary alignments = 4,073,954 (1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,873,996 number of mapped paired reads (second in pair) = 202,622,090 number of mapped paired reads (both in pair) = 404,648,054 number of mapped paired reads (singletons) = 1,848,032 number of mapped bases = 40,344,818,558 bp number of sequenced bases = 40,335,803,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,549,067 duplication rate = 11.85% >>>>>>> Insert size mean insert size = 72,497.3769 std insert size = 2,587,660.7764 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.9289 >>>>>>> ACTG content number of A's = 11,924,847,962 bp (29.56%) number of C's = 8,160,889,998 bp (20.23%) number of T's = 11,826,954,067 bp (29.32%) number of G's = 8,414,081,474 bp (20.86%) number of N's = 9,030,498 bp (0.02%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 189,474,348 number of insertions = 3,843,676 mapped reads with insertion percentage = 0.93% number of deletions = 3,905,946 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 13.0326X std coverageData = 16.8487X There is a 91.29% of reference with a coverageData >= 1X There is a 89.86% of reference with a coverageData >= 2X There is a 87.76% of reference with a coverageData >= 3X There is a 84.95% of reference with a coverageData >= 4X There is a 81.46% of reference with a coverageData >= 5X There is a 77.4% of reference with a coverageData >= 6X There is a 72.88% of reference with a coverageData >= 7X There is a 68.05% of reference with a coverageData >= 8X There is a 63.06% of reference with a coverageData >= 9X There is a 58.04% of reference with a coverageData >= 10X There is a 53.09% of reference with a coverageData >= 11X There is a 48.31% of reference with a coverageData >= 12X There is a 43.76% of reference with a coverageData >= 13X There is a 39.49% of reference with a coverageData >= 14X There is a 35.52% of reference with a coverageData >= 15X There is a 31.86% of reference with a coverageData >= 16X There is a 28.52% of reference with a coverageData >= 17X There is a 25.48% of reference with a coverageData >= 18X There is a 22.73% of reference with a coverageData >= 19X There is a 20.26% of reference with a coverageData >= 20X There is a 18.05% of reference with a coverageData >= 21X There is a 16.07% of reference with a coverageData >= 22X There is a 14.3% of reference with a coverageData >= 23X There is a 12.72% of reference with a coverageData >= 24X There is a 11.32% of reference with a coverageData >= 25X There is a 10.08% of reference with a coverageData >= 26X There is a 8.97% of reference with a coverageData >= 27X There is a 7.99% of reference with a coverageData >= 28X There is a 7.12% of reference with a coverageData >= 29X There is a 6.34% of reference with a coverageData >= 30X There is a 5.66% of reference with a coverageData >= 31X There is a 5.05% of reference with a coverageData >= 32X There is a 4.51% of reference with a coverageData >= 33X There is a 4.03% of reference with a coverageData >= 34X There is a 3.6% of reference with a coverageData >= 35X There is a 3.22% of reference with a coverageData >= 36X There is a 2.89% of reference with a coverageData >= 37X There is a 2.59% of reference with a coverageData >= 38X There is a 2.32% of reference with a coverageData >= 39X There is a 2.08% of reference with a coverageData >= 40X There is a 1.87% of reference with a coverageData >= 41X There is a 1.68% of reference with a coverageData >= 42X There is a 1.52% of reference with a coverageData >= 43X There is a 1.37% of reference with a coverageData >= 44X There is a 1.23% of reference with a coverageData >= 45X There is a 1.12% of reference with a coverageData >= 46X There is a 1.01% of reference with a coverageData >= 47X There is a 0.91% of reference with a coverageData >= 48X There is a 0.83% of reference with a coverageData >= 49X There is a 0.75% of reference with a coverageData >= 50X There is a 0.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3295725784 13.222537904930636 17.46698737995483 chr2 243199373 3731249909 15.342350035581712 15.80838146262821 chr3 198022430 2918421044 14.737830679080142 10.097616120049768 chr4 191154276 2691514297 14.080324820983863 14.515963806831696 chr5 180915260 2851974715 15.764146788944172 10.733640546205184 chr6 171115067 2446713501 14.298644437897453 12.704760962296652 chr7 159138663 2182638552 13.715325432889932 10.865243442710401 chr8 146364022 2067568423 14.126206664367286 10.571992564647598 chr9 141213431 1678954436 11.889481220805406 13.413389250216735 chr10 135534747 1869357008 13.792455804709622 18.771201810098788 chr11 135006516 1908984837 14.139945934165134 11.181045269519755 chr12 133851895 1919403538 14.33975617603322 10.471272582597763 chr13 115169878 1302925587 11.313076037121442 9.930324088169234 chr14 107349540 1296316537 12.07565991433219 10.956594570441885 chr15 102531392 1244937471 12.142012770098741 11.479473703298671 chr16 90354753 991985434 10.978785299761707 16.216853500116784 chr17 81195210 926541793 11.411286367754945 13.680655778711518 chr18 78077248 1092783979 13.996189760684189 18.036291181336708 chr19 59128983 560157097 9.473477617567006 12.15460976834063 chr20 63025520 767925953 12.184365206348158 11.532353959863865 chr21 48129895 520477360 10.81401403431277 21.277533024706045 chr22 51304566 405037295 7.89476116024449 10.12901943039231 chrMT 16571 69294768 4181.688974714863 1065.8269227995283 chrX 155270560 1347027345 8.675355746768737 7.061886194956913 chrY 59373566 256901895 4.32687325871584 16.81429059443969