BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238033.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 = 1,610,163 number of mapped reads = 1,234,404 (76.66%) number of supplementary alignments = 12,764 (0.79%) number of secondary alignments = 0 number of mapped bases = 81,765,353 bp number of sequenced bases = 81,730,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,319 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.644 >>>>>>> ACTG content number of A's = 22,274,115 bp (27.25%) number of C's = 15,372,446 bp (18.81%) number of T's = 25,691,168 bp (31.43%) number of G's = 18,382,463 bp (22.49%) number of N's = 10,738 bp (0.01%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 628,488 number of insertions = 5,644 mapped reads with insertion percentage = 0.45% number of deletions = 19,221 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2998X There is a 1.78% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 8230815 0.03302224470686474 0.5517790140376576 chr2 243199373 8793360 0.03615700111200534 0.3369093448343233 chr3 198022430 5824768 0.029414688022967903 0.24252796309455468 chr4 191154276 4561227 0.02386149604103023 0.22146572609186346 chr5 180915260 5150372 0.028468422177322133 0.23705497013557367 chr6 171115067 3867866 0.02260388911281553 0.23231403603957798 chr7 159138663 3619565 0.02274472420319379 0.2813592109401888 chr8 146364022 4036473 0.02757831429365886 0.3219980277601068 chr9 141213431 2905739 0.020576930816162946 0.26099302248362144 chr10 135534747 3021447 0.02229278518518945 0.3053401389253346 chr11 135006516 3064980 0.02270245978349667 0.24987600101624968 chr12 133851895 4084717 0.03051669160156455 0.24862495336521778 chr13 115169878 3082803 0.026767441743751782 0.2302283735907858 chr14 107349540 2200395 0.020497479542064177 0.21144251996889263 chr15 102531392 4595776 0.04482311134525512 0.301648543810316 chr16 90354753 1903303 0.02106478006751897 0.21584771137840128 chr17 81195210 2371802 0.029211107403995875 0.24710072637507463 chr18 78077248 1698923 0.021759514372227874 0.42781426701571856 chr19 59128983 1275945 0.021579011429978427 0.3712615621879446 chr20 63025520 1497927 0.023766991529780318 0.22122957913885374 chr21 48129895 1014345 0.021075155056955765 0.21164382988700922 chr22 51304566 777778 0.01516001519240997 0.17123784255260355 chrMT 16571 30709 1.853177237342345 2.0458579239040655 chrX 155270560 3955078 0.025472169353932903 0.23165335489006933 chrY 59373566 199240 0.003355702098135726 0.09168968436403732