BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716655.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,619,195 number of mapped reads = 2,339,264 (89.31%) number of supplementary alignments = 72,946 (2.79%) number of secondary alignments = 0 number of mapped bases = 172,263,748 bp number of sequenced bases = 172,203,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,858 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4352 >>>>>>> ACTG content number of A's = 45,034,904 bp (26.15%) number of C's = 36,096,625 bp (20.96%) number of T's = 50,771,636 bp (29.48%) number of G's = 40,280,069 bp (23.39%) number of N's = 20,157 bp (0.01%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,307,261 number of insertions = 16,049 mapped reads with insertion percentage = 0.68% number of deletions = 35,465 mapped reads with deletion percentage = 1.5% homopolymer indels = 39.22% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.477X There is a 4.74% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 14245347 0.057152704145118256 0.5889886070638087 chr2 243199373 16201245 0.06661713309598047 0.8384081493879623 chr3 198022430 12633624 0.06379895449217546 0.29870515011207915 chr4 191154276 7146261 0.037384782331523675 0.2336700704930232 chr5 180915260 10937641 0.060457260487589606 0.2864411928995906 chr6 171115067 12612812 0.07370953488274648 0.3702730172593015 chr7 159138663 9612627 0.0604040955151169 0.6968009040745162 chr8 146364022 12406280 0.08476318039415451 0.6485729743250639 chr9 141213431 7544280 0.05342466326733468 0.44801109087455265 chr10 135534747 7831823 0.05778461371237886 0.4329760171816106 chr11 135006516 7029811 0.05207016082097845 0.37831107778181267 chr12 133851895 5870200 0.043855934949594846 0.2396859608839594 chr13 115169878 6207941 0.05390247092212774 0.26228231502971433 chr14 107349540 4130760 0.03847953144466199 0.26232762247115726 chr15 102531392 3924533 0.03827640416702818 0.22074747170971393 chr16 90354753 4761345 0.05269612103305733 0.2939480733563335 chr17 81195210 5141572 0.06332358768454445 0.33985935604122397 chr18 78077248 5357321 0.06861564844088767 0.9752182915539784 chr19 59128983 3184970 0.05386478573460328 0.5688969322097163 chr20 63025520 3499379 0.055523207107216255 0.3008633938262456 chr21 48129895 3730553 0.07751010053107325 0.3342185818844037 chr22 51304566 2557241 0.04984431600103585 0.25997244330506836 chrMT 16571 57703 3.48216764226661 3.321971298027917 chrX 155270560 5274075 0.033966999281769834 0.28630449838039423 chrY 59373566 364404 0.0061374787561185055 0.1674457968093992