BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240061.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 = 2,311,323 number of mapped reads = 1,878,506 (81.27%) number of supplementary alignments = 14,704 (0.64%) number of secondary alignments = 0 number of mapped bases = 123,205,844 bp number of sequenced bases = 123,146,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 292,167 duplication rate = 11.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7964 >>>>>>> ACTG content number of A's = 35,615,067 bp (28.92%) number of C's = 23,589,192 bp (19.16%) number of T's = 38,250,408 bp (31.06%) number of G's = 25,680,570 bp (20.85%) number of N's = 10,966 bp (0.01%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,039,549 number of insertions = 9,014 mapped reads with insertion percentage = 0.48% number of deletions = 34,293 mapped reads with deletion percentage = 1.81% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.4751X There is a 1.55% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 10010176 0.040161087502365744 0.6327099370160314 chr2 243199373 13737955 0.05648844744348909 0.5613039950410297 chr3 198022430 7936379 0.04007818205240689 0.4148600715387287 chr4 191154276 7907373 0.041366445812595895 0.42206008908217807 chr5 180915260 6304529 0.034847966943197604 0.3813496375687867 chr6 171115067 6072281 0.03548653608626995 0.4025628500784204 chr7 159138663 7252483 0.04557335636280921 0.6154826545155707 chr8 146364022 7089018 0.04843415685857553 0.6526593536768347 chr9 141213431 4538644 0.03214031390541031 0.41295179007923005 chr10 135534747 5871512 0.04332108282166196 0.47228092886456774 chr11 135006516 5335809 0.03952260348678282 0.46013641946812883 chr12 133851895 6212522 0.04641340341128529 0.4406137385904998 chr13 115169878 2993834 0.02599493940594432 0.33537309402244925 chr14 107349540 4051737 0.03774340346497992 0.4129029922057139 chr15 102531392 3738027 0.03645739053264779 0.4050946444731428 chr16 90354753 3724075 0.041216149414962155 0.4095434469041289 chr17 81195210 2801462 0.03450279887200242 0.3860904520696522 chr18 78077248 2754931 0.035284683701966545 0.5606113317685992 chr19 59128983 2230985 0.03773081975720773 0.4707918114631451 chr20 63025520 2484559 0.03942147561813056 0.407788474953661 chr21 48129895 2026499 0.04210478747148732 0.42855840076402874 chr22 51304566 1088928 0.021224777537344336 0.2901206230131481 chrMT 16571 26047 1.5718423752338422 2.86545295753546 chrX 155270560 6708785 0.04320706385035257 0.4437408878801104 chrY 59373566 307294 0.00517560289371873 0.13499864369224224