BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063601.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 = 3,169,061 number of mapped reads = 3,065,792 (96.74%) number of supplementary alignments = 27,257 (0.86%) number of secondary alignments = 0 number of mapped bases = 215,867,512 bp number of sequenced bases = 215,777,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 225,673 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9 >>>>>>> ACTG content number of A's = 63,707,767 bp (29.52%) number of C's = 40,155,815 bp (18.61%) number of T's = 66,197,522 bp (30.68%) number of G's = 45,689,361 bp (21.17%) number of N's = 27,315 bp (0.01%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,055,208 number of insertions = 14,330 mapped reads with insertion percentage = 0.46% number of deletions = 49,249 mapped reads with deletion percentage = 1.59% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 0.0697X std coverageData = 0.685X There is a 5.23% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20167051 0.08091073522340392 1.3795435864181769 chr2 243199373 21401267 0.08799885762863377 0.6042687150133457 chr3 198022430 13659843 0.06898129166478767 0.3312942566929798 chr4 191154276 12570243 0.06575967466194688 0.33238519777069125 chr5 180915260 9085049 0.05021715138899836 0.28063662921464555 chr6 171115067 18211203 0.10642664798185189 0.4609729068114911 chr7 159138663 18297239 0.1149767043097503 1.2524584806266543 chr8 146364022 9693720 0.06623021059096067 1.2613526041996506 chr9 141213431 4997810 0.03539188846703965 0.5024803856498707 chr10 135534747 9307857 0.06867506086833954 0.43214597489751944 chr11 135006516 10193396 0.07550299275925319 0.46139537128123753 chr12 133851895 9666417 0.07221725923267654 0.3655701551868044 chr13 115169878 6532819 0.05672333003600125 0.30542706203196246 chr14 107349540 3592134 0.03346203439716649 0.2819838082496787 chr15 102531392 4159592 0.04056896057745905 0.24943840480346235 chr16 90354753 3308204 0.036613502778320914 0.2691501432564269 chr17 81195210 6096456 0.07508393660167885 0.37872920527725423 chr18 78077248 5817632 0.07451123277295839 0.8843267510028366 chr19 59128983 3901889 0.06598944886300513 0.8671167040548231 chr20 63025520 3445802 0.05467312288736372 0.33335163625518055 chr21 48129895 3790629 0.07875830603827413 0.3665620958585924 chr22 51304566 1463887 0.0285332693390292 0.20517890020914115 chrMT 16571 127489 7.693500693983465 5.575505372298717 chrX 155270560 15812286 0.10183698699869441 0.45252478048626893 chrY 59373566 567598 0.009559776146846225 0.31736509696210363