BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230393.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,726,226 number of mapped reads = 2,374,368 (87.09%) number of supplementary alignments = 19,376 (0.71%) number of secondary alignments = 0 number of mapped bases = 151,534,036 bp number of sequenced bases = 151,471,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,594 duplication rate = 5.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8647 >>>>>>> ACTG content number of A's = 41,517,352 bp (27.41%) number of C's = 26,976,632 bp (17.81%) number of T's = 48,695,853 bp (32.15%) number of G's = 34,213,623 bp (22.59%) number of N's = 67,807 bp (0.04%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,304,763 number of insertions = 11,744 mapped reads with insertion percentage = 0.49% number of deletions = 37,899 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.4343X There is a 3.97% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 13602676 0.05457429131139457 0.8115495604522989 chr2 243199373 13243202 0.054454095981571464 0.49469295030286575 chr3 198022430 10770056 0.05438806098884859 0.2758944129053558 chr4 191154276 7948990 0.041584160011152456 0.2651922752162299 chr5 180915260 10871484 0.06009158099764497 0.29074265488828976 chr6 171115067 9074749 0.053033021341130644 0.34535303941175777 chr7 159138663 9853340 0.06191669462498878 0.6101941477767809 chr8 146364022 8269908 0.05650232814728199 0.518644936056115 chr9 141213431 6714062 0.047545491618286646 0.4162222334275287 chr10 135534747 5456314 0.04025767650564176 0.3778724412240105 chr11 135006516 6568240 0.04865128139444766 0.3634287111727054 chr12 133851895 6332048 0.0473063754532575 0.26621812297587616 chr13 115169878 4625564 0.04016296691744346 0.2357514207994928 chr14 107349540 4731185 0.044072708648774835 0.2707820785631044 chr15 102531392 3908991 0.03812482132301491 0.23973248720020598 chr16 90354753 3975634 0.044000275226251793 0.2914463538279188 chr17 81195210 2902034 0.03574144336839575 0.24916081501619314 chr18 78077248 4553643 0.058322278469650976 0.7679995622573851 chr19 59128983 2362489 0.03995483906767008 0.5672191307037809 chr20 63025520 2984352 0.04735148555696169 0.27532906510458277 chr21 48129895 2333594 0.04848533328402233 0.2832789732040429 chr22 51304566 1228447 0.023944204108460834 0.1818173430634962 chrMT 16571 11108 0.6703276808882989 0.9617450984120622 chrX 155270560 8802276 0.0566899224167157 0.3217828627526425 chrY 59373566 409650 0.0068995350557182296 0.15469936775896923