BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124860.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 = 195,897,960 number of mapped reads = 191,155,007 (97.58%) number of supplementary alignments = 29,274,787 (14.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 95,595,680 number of mapped paired reads (second in pair) = 95,559,327 number of mapped paired reads (both in pair) = 190,403,154 number of mapped paired reads (singletons) = 751,853 number of mapped bases = 19,029,736,001 bp number of sequenced bases = 19,012,204,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,404,372 duplication rate = 44.69% >>>>>>> Insert size mean insert size = 587,009.4986 std insert size = 7,416,196.4785 median insert size = 98 >>>>>>> Mapping quality mean mapping quality = 45.6196 >>>>>>> ACTG content number of A's = 5,442,873,502 bp (28.63%) number of C's = 4,057,900,034 bp (21.34%) number of T's = 5,268,010,879 bp (27.71%) number of G's = 4,240,772,457 bp (22.31%) number of N's = 2,647,323 bp (0.01%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 275,488,826 number of insertions = 6,130,829 mapped reads with insertion percentage = 3.04% number of deletions = 6,936,418 mapped reads with deletion percentage = 3.45% homopolymer indels = 34.9% >>>>>>> Coverage mean coverageData = 6.1472X std coverageData = 269.393X There is a 70.95% of reference with a coverageData >= 1X There is a 65.38% of reference with a coverageData >= 2X There is a 48.67% of reference with a coverageData >= 3X There is a 43.24% of reference with a coverageData >= 4X There is a 34.05% of reference with a coverageData >= 5X There is a 30.24% of reference with a coverageData >= 6X There is a 25.35% of reference with a coverageData >= 7X There is a 22.72% of reference with a coverageData >= 8X There is a 19.81% of reference with a coverageData >= 9X There is a 17.85% of reference with a coverageData >= 10X There is a 15.83% of reference with a coverageData >= 11X There is a 14.26% of reference with a coverageData >= 12X There is a 12.69% of reference with a coverageData >= 13X There is a 11.38% of reference with a coverageData >= 14X There is a 10.11% of reference with a coverageData >= 15X There is a 9.02% of reference with a coverageData >= 16X There is a 7.98% of reference with a coverageData >= 17X There is a 7.07% of reference with a coverageData >= 18X There is a 6.23% of reference with a coverageData >= 19X There is a 5.49% of reference with a coverageData >= 20X There is a 4.82% of reference with a coverageData >= 21X There is a 4.23% of reference with a coverageData >= 22X There is a 3.7% of reference with a coverageData >= 23X There is a 3.24% of reference with a coverageData >= 24X There is a 2.84% of reference with a coverageData >= 25X There is a 2.49% of reference with a coverageData >= 26X There is a 2.18% of reference with a coverageData >= 27X There is a 1.91% of reference with a coverageData >= 28X There is a 1.68% of reference with a coverageData >= 29X There is a 1.48% of reference with a coverageData >= 30X There is a 1.3% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.02% of reference with a coverageData >= 33X There is a 0.91% of reference with a coverageData >= 34X There is a 0.81% of reference with a coverageData >= 35X There is a 0.73% of reference with a coverageData >= 36X There is a 0.66% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.54% of reference with a coverageData >= 39X There is a 0.49% of reference with a coverageData >= 40X There is a 0.45% of reference with a coverageData >= 41X There is a 0.42% of reference with a coverageData >= 42X There is a 0.38% of reference with a coverageData >= 43X There is a 0.36% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.29% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.26% of reference with a coverageData >= 49X There is a 0.25% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1765808697 7.084470601980968 776.6992888489342 chr2 243199373 1474040555 6.061037645027152 127.71765947035864 chr3 198022430 1173382468 5.925502823089284 64.64605170996447 chr4 191154276 1109379304 5.803580893999985 142.3685559208916 chr5 180915260 978110214 5.406455011036659 16.068854363429114 chr6 171115067 951967095 5.563315444337815 69.7361051041665 chr7 159138663 1309953307 8.231521380822459 206.354131338611 chr8 146364022 1119187301 7.646601164048362 90.96424447713397 chr9 141213431 835443595 5.9161765922959555 172.50420813976214 chr10 135534747 1248628593 9.212608726823388 490.07860433483876 chr11 135006516 699062339 5.17798962384897 68.86976049559179 chr12 133851895 859456546 6.420951649582548 23.998103931405378 chr13 115169878 402762809 3.497119350946955 5.915637032270998 chr14 107349540 507255306 4.725267625739244 17.526917989267734 chr15 102531392 395307197 3.855474789613702 15.534355210872162 chr16 90354753 672053318 7.437940957018609 95.95149089460732 chr17 81195210 496921852 6.120088266290585 83.33116165583579 chr18 78077248 421936990 5.404096594183238 265.625802016225 chr19 59128983 566529640 9.58125121144059 388.64359276141016 chr20 63025520 315125470 4.999966204166185 47.98403944974763 chr21 48129895 221244072 4.596811856747246 91.0868617760088 chr22 51304566 195372335 3.8080886406874583 41.093447029040604 chrMT 16571 63402629 3826.1196668879365 1734.63856940173 chrX 155270560 808394637 5.206361315371053 42.96925462259278 chrY 59373566 439009732 7.394026695314207 191.57372376199424