BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716605.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 = 2,057,824 number of mapped reads = 1,933,723 (93.97%) number of supplementary alignments = 46,765 (2.27%) number of secondary alignments = 0 number of mapped bases = 149,138,734 bp number of sequenced bases = 149,081,729 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,864 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6532 >>>>>>> ACTG content number of A's = 38,608,747 bp (25.9%) number of C's = 31,384,744 bp (21.05%) number of T's = 44,140,153 bp (29.61%) number of G's = 34,929,729 bp (23.43%) number of N's = 18,356 bp (0.01%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,127,241 number of insertions = 11,430 mapped reads with insertion percentage = 0.58% number of deletions = 32,845 mapped reads with deletion percentage = 1.68% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0482X std coverageData = 0.4031X There is a 4.11% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 12779601 0.051272092918877826 0.6109120998954458 chr2 243199373 14177747 0.05829680736882492 0.622172259355707 chr3 198022430 11487061 0.05800888818504045 0.280169573142661 chr4 191154276 6334803 0.03313973996584832 0.22572904264712274 chr5 180915260 8770548 0.0484787629302249 0.2530420642878109 chr6 171115067 11245927 0.06572143059734184 0.3403939793036095 chr7 159138663 7798991 0.049007518681993704 0.5703796977866484 chr8 146364022 10152728 0.06936628183120029 0.485892763819045 chr9 141213431 6442129 0.045619803685670667 0.359755331471257 chr10 135534747 7579012 0.05591932820002239 0.38528981260635464 chr11 135006516 5953532 0.04409810856833014 0.3305781549922221 chr12 133851895 4090544 0.030560224791737166 0.202708392916747 chr13 115169878 5476420 0.047550801434382 0.24918405805651508 chr14 107349540 3455832 0.03219233170444885 0.24502880103925945 chr15 102531392 3191086 0.031123014500768702 0.1998008214806682 chr16 90354753 3629459 0.04016898812174275 0.26215166086168645 chr17 81195210 4859036 0.05984387502661795 0.3036591737613042 chr18 78077248 4760695 0.06097416497056864 0.7381218180247361 chr19 59128983 2745127 0.04642608177448274 0.5008444511601481 chr20 63025520 2868108 0.045507089826470296 0.27491739545839916 chr21 48129895 3319991 0.06897980974194937 0.31456944432205974 chr22 51304566 2310906 0.04504289150404274 0.24501965700851516 chrMT 16571 43558 2.628567980206385 2.4697269665337984 chrX 155270560 5339002 0.03438515324476192 0.26082414091011624 chrY 59373566 326891 0.005505665602096394 0.15724538608203134