BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008687.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 = 2,027,042 number of mapped reads = 1,776,620 (87.65%) number of supplementary alignments = 8,748 (0.43%) number of secondary alignments = 0 number of mapped bases = 113,103,336 bp number of sequenced bases = 113,032,940 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,813 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1566 >>>>>>> ACTG content number of A's = 29,175,229 bp (25.81%) number of C's = 21,284,024 bp (18.83%) number of T's = 34,789,079 bp (30.78%) number of G's = 27,737,350 bp (24.54%) number of N's = 47,258 bp (0.04%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 972,192 number of insertions = 7,735 mapped reads with insertion percentage = 0.43% number of deletions = 40,326 mapped reads with deletion percentage = 2.24% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.4118X There is a 3.24% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9573564 0.03840938875735038 0.895531393409791 chr2 243199373 9419253 0.0387305809378053 0.46461086379044053 chr3 198022430 9231574 0.04661882999819768 0.2633813073881582 chr4 191154276 5966348 0.03121221311314009 0.20858315290850843 chr5 180915260 5520869 0.030516325709616758 0.19215216301819948 chr6 171115067 5041675 0.029463653250359302 0.22141706336599812 chr7 159138663 6401697 0.04022716340151733 0.47488557861339437 chr8 146364022 8035528 0.054900978329223554 0.3528200455094119 chr9 141213431 3717800 0.026327524044083315 0.3201766974624433 chr10 135534747 7216367 0.053243667470748296 0.6536511163347558 chr11 135006516 4162988 0.030835459823287344 0.29799089384116034 chr12 133851895 4691928 0.03505313092504219 0.2077294701023835 chr13 115169878 2881299 0.025017817592895255 0.1694234538094342 chr14 107349540 5032574 0.04688025677613523 0.24436443400928162 chr15 102531392 2718411 0.02651296297625609 0.18195437124543712 chr16 90354753 3369381 0.03729057839381178 0.2634720693828094 chr17 81195210 3369312 0.041496438028795046 0.2746111731846011 chr18 78077248 1720919 0.022041235367312128 0.5585684543763328 chr19 59128983 2644551 0.0447251223651183 0.5803227304174283 chr20 63025520 2751580 0.043658187984803615 0.23515411965918154 chr21 48129895 1163800 0.024180397650981785 0.18553382989593922 chr22 51304566 1444803 0.02816129464968089 0.18235974683950826 chrMT 16571 130691 7.886729829219721 5.107949878144402 chrX 155270560 6541463 0.04212944810658247 0.26845093176396684 chrY 59373566 354961 0.00597843491495862 0.16149097431794596