BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438264.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 593,284,296 number of mapped reads = 591,560,069 (99.71%) number of supplementary alignments = 9,136,384 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 295,903,514 number of mapped paired reads (second in pair) = 295,656,555 number of mapped paired reads (both in pair) = 590,372,400 number of mapped paired reads (singletons) = 1,187,669 number of mapped bases = 85,058,894,654 bp number of sequenced bases = 85,034,756,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,265,421 duplication rate = 41.24% >>>>>>> Insert size mean insert size = 39,896.1887 std insert size = 1,947,526.0186 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.8871 >>>>>>> ACTG content number of A's = 25,726,186,076 bp (30.25%) number of C's = 16,975,672,213 bp (19.96%) number of T's = 24,577,492,897 bp (28.9%) number of G's = 17,754,882,753 bp (20.88%) number of N's = 522,750 bp (0%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 437,501,084 number of insertions = 11,056,230 mapped reads with insertion percentage = 1.84% number of deletions = 9,794,355 mapped reads with deletion percentage = 1.63% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 27.4765X std coverageData = 114.7352X There is a 89.93% of reference with a coverageData >= 1X There is a 88.88% of reference with a coverageData >= 2X There is a 87.69% of reference with a coverageData >= 3X There is a 86.45% of reference with a coverageData >= 4X There is a 85.05% of reference with a coverageData >= 5X There is a 83.54% of reference with a coverageData >= 6X There is a 81.91% of reference with a coverageData >= 7X There is a 80.18% of reference with a coverageData >= 8X There is a 78.35% of reference with a coverageData >= 9X There is a 76.45% of reference with a coverageData >= 10X There is a 74.47% of reference with a coverageData >= 11X There is a 72.44% of reference with a coverageData >= 12X There is a 70.36% of reference with a coverageData >= 13X There is a 68.26% of reference with a coverageData >= 14X There is a 66.13% of reference with a coverageData >= 15X There is a 63.99% of reference with a coverageData >= 16X There is a 61.85% of reference with a coverageData >= 17X There is a 59.73% of reference with a coverageData >= 18X There is a 57.62% of reference with a coverageData >= 19X There is a 55.53% of reference with a coverageData >= 20X There is a 53.47% of reference with a coverageData >= 21X There is a 51.45% of reference with a coverageData >= 22X There is a 49.46% of reference with a coverageData >= 23X There is a 47.52% of reference with a coverageData >= 24X There is a 45.63% of reference with a coverageData >= 25X There is a 43.78% of reference with a coverageData >= 26X There is a 41.98% of reference with a coverageData >= 27X There is a 40.24% of reference with a coverageData >= 28X There is a 38.55% of reference with a coverageData >= 29X There is a 36.91% of reference with a coverageData >= 30X There is a 35.33% of reference with a coverageData >= 31X There is a 33.8% of reference with a coverageData >= 32X There is a 32.33% of reference with a coverageData >= 33X There is a 30.91% of reference with a coverageData >= 34X There is a 29.54% of reference with a coverageData >= 35X There is a 28.22% of reference with a coverageData >= 36X There is a 26.96% of reference with a coverageData >= 37X There is a 25.75% of reference with a coverageData >= 38X There is a 24.58% of reference with a coverageData >= 39X There is a 23.46% of reference with a coverageData >= 40X There is a 22.39% of reference with a coverageData >= 41X There is a 21.37% of reference with a coverageData >= 42X There is a 20.39% of reference with a coverageData >= 43X There is a 19.45% of reference with a coverageData >= 44X There is a 18.55% of reference with a coverageData >= 45X There is a 17.69% of reference with a coverageData >= 46X There is a 16.87% of reference with a coverageData >= 47X There is a 16.09% of reference with a coverageData >= 48X There is a 15.34% of reference with a coverageData >= 49X There is a 14.63% of reference with a coverageData >= 50X There is a 13.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6981882928 28.01149662130631 29.388263436740335 chr2 243199373 7431044572 30.555360732776233 110.21880499946866 chr3 198022430 6202350039 31.32145201429959 267.0648584562884 chr4 191154276 5655978470 29.588553227027994 36.47045586518546 chr5 180915260 5474222869 30.258491566714714 68.04052284626931 chr6 171115067 5054361126 29.53779123377838 29.159673692135748 chr7 159138663 4706920271 29.577477793689898 34.64818041343469 chr8 146364022 4556681401 31.132523817909295 29.84735610339505 chr9 141213431 3556658888 25.186406581963155 35.876712476444965 chr10 135534747 4279410971 31.574272027821767 49.14602384360381 chr11 135006516 3968893890 29.397795066424795 25.9818413661457 chr12 133851895 3902431239 29.154844905258905 25.679449338503467 chr13 115169878 2919719027 25.35141199854358 25.86498006591251 chr14 107349540 2723322469 25.368739064927524 32.810628081892524 chr15 102531392 2477326813 24.161642250989825 26.81329727962016 chr16 90354753 2287902292 25.32132750116643 46.55516179453109 chr17 81195210 2101024809 25.876216207828023 32.042791861864444 chr18 78077248 2300351929 29.46251293334519 27.499671325598857 chr19 59128983 1450025304 24.52308885474996 378.66570658436797 chr20 63025520 1850559097 29.36205995603051 28.19330534499287 chr21 48129895 1096605145 22.784282928520827 110.63528599638047 chr22 51304566 902662147 17.59418736726084 23.472551205200304 chrMT 16571 398908181 24072.667974171745 9701.777644242426 chrX 155270560 2414170431 15.548153049747485 37.17380730045746 chrY 59373566 365480346 6.155607126578855 23.86930739513058