BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063550.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 = 2,685,069 number of mapped reads = 2,413,866 (89.9%) number of supplementary alignments = 16,916 (0.63%) number of secondary alignments = 0 number of mapped bases = 160,234,344 bp number of sequenced bases = 160,156,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,061 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.02 >>>>>>> ACTG content number of A's = 44,855,087 bp (28.01%) number of C's = 29,211,353 bp (18.24%) number of T's = 50,684,811 bp (31.65%) number of G's = 35,401,826 bp (22.1%) number of N's = 3,507 bp (0%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,274,053 number of insertions = 12,318 mapped reads with insertion percentage = 0.51% number of deletions = 47,303 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.485X There is a 4.2% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% 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 18223468 0.07311302947566177 0.9972021929199139 chr2 243199373 13870600 0.05703386414569416 0.6116947760876281 chr3 198022430 10297840 0.05200340183685252 0.2694141270709726 chr4 191154276 8066718 0.04220003951154093 0.2566231109621723 chr5 180915260 6566448 0.03629571104173302 0.2273384201735921 chr6 171115067 12270914 0.07171147588073001 0.37829990449559164 chr7 159138663 11324368 0.07116038168549901 0.6084381681085339 chr8 146364022 4541668 0.031029948056497107 0.6329780020306033 chr9 141213431 5271992 0.03733350264678435 0.4178400634160687 chr10 135534747 9055082 0.06681004097052691 0.40733854308036166 chr11 135006516 7766677 0.05752816404802269 0.3816606675718587 chr12 133851895 6142265 0.04588851730489135 0.2650278627539444 chr13 115169878 3645610 0.031654196942016384 0.2112214143397589 chr14 107349540 3578738 0.033337245786055535 0.2610951789461563 chr15 102531392 2806567 0.02737275818902371 0.2040074237275793 chr16 90354753 3412927 0.0377725231565848 0.25794706855962235 chr17 81195210 5182941 0.06383308818340393 0.32631938959944234 chr18 78077248 4754737 0.06089785592852863 0.698020945842283 chr19 59128983 3559670 0.060201779557074404 0.6766711382957541 chr20 63025520 2535703 0.04023295642780893 0.24600734139271427 chr21 48129895 2737142 0.05686989344148787 0.2960355383636774 chr22 51304566 1619569 0.03156773609584769 0.20695819650603928 chrMT 16571 23915 1.4431838754450546 1.6296393212675857 chrX 155270560 12570225 0.08095691159998393 0.4044420236272338 chrY 59373566 408560 0.006881176717598535 0.16197563237487675