BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354885.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 25,046,022 number of mapped reads = 19,938,228 (79.61%) number of supplementary alignments = 461,392 (1.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,971,698 number of mapped paired reads (second in pair) = 9,966,530 number of mapped paired reads (both in pair) = 19,805,098 number of mapped paired reads (singletons) = 133,130 number of mapped bases = 2,709,663,865 bp number of sequenced bases = 2,707,446,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,595,435 duplication rate = 60.81% >>>>>>> Insert size mean insert size = 150,532.0334 std insert size = 4,014,564.1863 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 53.4979 >>>>>>> ACTG content number of A's = 658,034,311 bp (24.3%) number of C's = 671,048,423 bp (24.79%) number of T's = 657,354,491 bp (24.28%) number of G's = 721,001,947 bp (26.63%) number of N's = 7,391 bp (0%) GC percentage = 51.42% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 40,390,115 number of insertions = 543,791 mapped reads with insertion percentage = 2.62% number of deletions = 1,361,185 mapped reads with deletion percentage = 6.51% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.8753X std coverageData = 32.2472X There is a 3.44% of reference with a coverageData >= 1X There is a 2.99% of reference with a coverageData >= 2X There is a 2.56% of reference with a coverageData >= 3X There is a 2.35% of reference with a coverageData >= 4X There is a 2.12% of reference with a coverageData >= 5X There is a 1.98% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.61% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 1.45% of reference with a coverageData >= 11X There is a 1.38% of reference with a coverageData >= 12X There is a 1.32% of reference with a coverageData >= 13X There is a 1.26% of reference with a coverageData >= 14X There is a 1.21% of reference with a coverageData >= 15X There is a 1.16% of reference with a coverageData >= 16X There is a 1.12% of reference with a coverageData >= 17X There is a 1.08% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 1% of reference with a coverageData >= 20X There is a 0.97% of reference with a coverageData >= 21X There is a 0.94% of reference with a coverageData >= 22X There is a 0.91% of reference with a coverageData >= 23X There is a 0.88% of reference with a coverageData >= 24X There is a 0.85% of reference with a coverageData >= 25X There is a 0.83% of reference with a coverageData >= 26X There is a 0.8% of reference with a coverageData >= 27X There is a 0.78% of reference with a coverageData >= 28X There is a 0.76% of reference with a coverageData >= 29X There is a 0.74% of reference with a coverageData >= 30X There is a 0.72% of reference with a coverageData >= 31X There is a 0.7% of reference with a coverageData >= 32X There is a 0.68% of reference with a coverageData >= 33X There is a 0.66% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.63% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.59% of reference with a coverageData >= 39X There is a 0.57% of reference with a coverageData >= 40X There is a 0.56% of reference with a coverageData >= 41X There is a 0.55% of reference with a coverageData >= 42X There is a 0.53% of reference with a coverageData >= 43X There is a 0.52% of reference with a coverageData >= 44X There is a 0.51% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.48% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 420828913 1.688376587836064 15.83954299982301 chr2 243199373 151364762 0.6223896062429405 70.79606405668908 chr3 198022430 158376657 0.7997915034170624 9.360650925865261 chr4 191154276 91517416 0.47876206546381417 8.158826592172927 chr5 180915260 106821631 0.5904511924533066 7.725770252933208 chr6 171115067 70231458 0.41043409695769223 6.348500183038765 chr7 159138663 120169861 0.7551267475459437 20.8914705163219 chr8 146364022 85365178 0.583238809876378 7.932031932329653 chr9 141213431 139727907 0.9894802924234594 13.526297340990943 chr10 135534747 99764906 0.7360836110905198 13.440546248684164 chr11 135006516 131232913 0.9720487342996097 10.935139404123685 chr12 133851895 140066817 1.046431333676673 10.76120231722229 chr13 115169878 87833181 0.7626402191725861 9.809488777630998 chr14 107349540 106891624 0.9957343459506207 14.50721007203532 chr15 102531392 147089776 1.4345828446374744 13.108198361575045 chr16 90354753 81810340 0.9054348253267872 9.82961212950884 chr17 81195210 91993244 1.132988559300481 11.406581267945219 chr18 78077248 98497929 1.2615445795425577 131.79297709998445 chr19 59128983 77607482 1.3125117000574829 11.841433220176807 chr20 63025520 93337123 1.4809417359825037 13.266924827808207 chr21 48129895 24826483 0.5158225049109291 7.745335892911795 chr22 51304566 68367175 1.3325748628299476 12.928047095368955 chrMT 16571 555889 33.54589342827832 23.97542046031308 chrX 155270560 37447850 0.2411780443118129 4.233772442849868 chrY 59373566 77937350 1.3126607554614456 67.23708030832594