BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237817.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 = 3,469,743 number of mapped reads = 3,108,796 (89.6%) number of supplementary alignments = 30,267 (0.87%) number of secondary alignments = 0 number of mapped bases = 223,300,932 bp number of sequenced bases = 223,204,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 313,205 duplication rate = 7.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0715 >>>>>>> ACTG content number of A's = 67,760,821 bp (30.36%) number of C's = 43,732,113 bp (19.59%) number of T's = 67,015,699 bp (30.02%) number of G's = 44,326,361 bp (19.86%) number of N's = 369,347 bp (0.17%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,948,766 number of insertions = 16,226 mapped reads with insertion percentage = 0.52% number of deletions = 53,844 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.08% >>>>>>> Coverage mean coverageData = 0.0721X std coverageData = 1.1322X There is a 1.97% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 22343836 0.08964405348462502 2.3683935418700828 chr2 243199373 18749103 0.07709354990812414 0.9623613230387527 chr3 198022430 18328852 0.09255947419693819 0.8638063555893117 chr4 191154276 11691955 0.06116501940035074 0.7073307298522219 chr5 180915260 13988721 0.07732195172480198 0.7979920703580584 chr6 171115067 15482091 0.09047766085963663 0.9233958499523502 chr7 159138663 12565015 0.07895639414791364 1.2492767684555057 chr8 146364022 10511401 0.07181683624408736 1.4764332026849583 chr9 141213431 8529853 0.06040397814567652 0.875293340557545 chr10 135534747 11414409 0.0842175844398042 1.194138416129233 chr11 135006516 9825107 0.07277505776091578 0.9920746168499923 chr12 133851895 8671872 0.06478706932016166 0.7147366515498546 chr13 115169878 7485987 0.0649995218367775 0.7277047709278944 chr14 107349540 5329023 0.04964178700719165 0.679470747449475 chr15 102531392 4259904 0.04154731460195137 0.5753020023612339 chr16 90354753 4150120 0.04593139665823667 0.6519357504023917 chr17 81195210 4866547 0.05993638048352852 0.8221664537246672 chr18 78077248 4450841 0.057005608087006346 1.5156282760720778 chr19 59128983 3008171 0.05087472923388518 1.3357885531194058 chr20 63025520 3921496 0.06222076390643028 0.6980463328991153 chr21 48129895 2990146 0.06212658473491372 0.7216810433385922 chr22 51304566 1574846 0.030696020311330573 0.5030619104983863 chrMT 16571 109745 6.622714380544324 5.985012087168665 chrX 155270560 18433274 0.11871712190643223 1.0469766606992825 chrY 59373566 618617 0.010419064268432185 0.3278467703481105