BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236082.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 = 1,261,549 number of mapped reads = 1,052,608 (83.44%) number of supplementary alignments = 5,703 (0.45%) number of secondary alignments = 0 number of mapped bases = 68,522,878 bp number of sequenced bases = 68,489,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,374 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4727 >>>>>>> ACTG content number of A's = 18,269,118 bp (26.67%) number of C's = 12,252,705 bp (17.89%) number of T's = 22,135,395 bp (32.32%) number of G's = 15,798,667 bp (23.07%) number of N's = 33,287 bp (0.05%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 569,624 number of insertions = 4,933 mapped reads with insertion percentage = 0.46% number of deletions = 19,622 mapped reads with deletion percentage = 1.84% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2299X There is a 1.93% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6026269 0.024177548588735512 0.3141220963520596 chr2 243199373 5838024 0.024005094782871828 0.28008821832647374 chr3 198022430 5766884 0.029122377702364324 0.1897609684469345 chr4 191154276 2796693 0.014630554223123943 0.1594781699375964 chr5 180915260 2914310 0.01610870194145038 0.14181616149576526 chr6 171115067 7290744 0.04260725912581386 0.313172175203293 chr7 159138663 3135433 0.019702521944651503 0.19656872152437735 chr8 146364022 5367137 0.03666978350731575 0.4210373468452972 chr9 141213431 2619899 0.01855276074979015 0.21866058110490708 chr10 135534747 3176420 0.023436204149183973 0.21807492862820513 chr11 135006516 2385266 0.01766778427198284 0.19559958629115995 chr12 133851895 2516694 0.018802079716540434 0.1576064704957691 chr13 115169878 3179198 0.027604422746718548 0.18647342707114037 chr14 107349540 1900079 0.01769992679987264 0.15070003196979204 chr15 102531392 2093098 0.020414216165133114 0.16744857770402463 chr16 90354753 1123056 0.012429407006402863 0.1335388683491891 chr17 81195210 1511961 0.018621307833306917 0.16240175590755895 chr18 78077248 1828275 0.023416232600821176 0.34553841599400625 chr19 59128983 1268646 0.021455569428616757 0.22145557722321244 chr20 63025520 866614 0.013750207852311255 0.13337345486240748 chr21 48129895 999944 0.020775943932560003 0.16992574529050244 chr22 51304566 492313 0.009595890549001038 0.10723627125814977 chrMT 16571 26807 1.6177056303180255 1.7581275383148292 chrX 155270560 3229409 0.020798591825778177 0.17178474785776804 chrY 59373566 169705 0.0028582585051401496 0.08752973242256384