BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230356.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 = 2,158,569 number of mapped reads = 1,589,770 (73.65%) number of supplementary alignments = 9,888 (0.46%) number of secondary alignments = 0 number of mapped bases = 103,375,927 bp number of sequenced bases = 103,330,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,443 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0814 >>>>>>> ACTG content number of A's = 27,704,488 bp (26.81%) number of C's = 17,809,893 bp (17.24%) number of T's = 34,422,865 bp (33.31%) number of G's = 23,198,638 bp (22.45%) number of N's = 195,101 bp (0.19%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 973,397 number of insertions = 9,378 mapped reads with insertion percentage = 0.58% number of deletions = 27,383 mapped reads with deletion percentage = 1.71% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3339X There is a 2.8% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 4727143 0.018965421153353916 0.4236078497264621 chr2 243199373 5442378 0.022378256707100967 0.3028082770290339 chr3 198022430 12599142 0.0636248227031655 0.2903335574056804 chr4 191154276 7672452 0.04013748559828188 0.24890170267847248 chr5 180915260 5011266 0.027699520759055924 0.19144514497769688 chr6 171115067 3288178 0.01921618041969384 0.20756973718813573 chr7 159138663 4698673 0.02952565336055387 0.613775338722024 chr8 146364022 6241409 0.04264305472556637 0.5228413130335983 chr9 141213431 3572784 0.02530059623011355 0.2836145528777672 chr10 135534747 5750303 0.04242678078707005 0.35236143184332963 chr11 135006516 7049265 0.05221425756961242 0.41902707718796534 chr12 133851895 5844542 0.04366424547071224 0.24159272846073346 chr13 115169878 1667141 0.014475495059567573 0.1371649897561717 chr14 107349540 2983607 0.027793384116969667 0.20702805934416527 chr15 102531392 1462831 0.014267152444394787 0.136396227947047 chr16 90354753 4076880 0.04512081395430299 0.2730399182279264 chr17 81195210 2175879 0.026798120233939907 0.2294834811484652 chr18 78077248 3495760 0.0447730944615261 0.5790111974084898 chr19 59128983 1469170 0.024846867398345074 0.3413018475702284 chr20 63025520 2612612 0.041453239893935026 0.24704073949935762 chr21 48129895 2353596 0.04890091698724878 0.2734446569032711 chr22 51304566 1081607 0.02108208068654162 0.16702689838111348 chrMT 16571 29394 1.7738217367690543 1.5725014113752305 chrX 155270560 7748034 0.049900212892901266 0.28602812140055056 chrY 59373566 321881 0.005421284616793945 0.12593856772763276