BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237266.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 = 2,353,043 number of mapped reads = 437,471 (18.59%) number of supplementary alignments = 3,259 (0.14%) number of secondary alignments = 0 number of mapped bases = 28,204,410 bp number of sequenced bases = 28,192,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,728 duplication rate = 6.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1418 >>>>>>> ACTG content number of A's = 7,598,907 bp (26.95%) number of C's = 5,164,198 bp (18.32%) number of T's = 9,017,997 bp (31.99%) number of G's = 6,410,522 bp (22.74%) number of N's = 383 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 259,829 number of insertions = 2,029 mapped reads with insertion percentage = 0.46% number of deletions = 6,987 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 0.1436X There is a 0.68% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.05% 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% 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 2262660 0.009077851003628994 0.1921015504616558 chr2 243199373 2320794 0.009542763089278195 0.15959324637352884 chr3 198022430 2004052 0.010120328288063125 0.13403366899511093 chr4 191154276 1695703 0.008870860937476492 0.13133611599663098 chr5 180915260 1898415 0.010493393426292508 0.13747947740089317 chr6 171115067 2010047 0.011746756350801066 0.14695792247953987 chr7 159138663 1544999 0.009708508107800303 0.15231785759728128 chr8 146364022 1483554 0.010136056523508215 0.1510861394423996 chr9 141213431 1381761 0.009784912031490829 0.14779074310245538 chr10 135534747 1171752 0.008645399249537094 0.13906268538518182 chr11 135006516 1185276 0.00877939846992274 0.13044461181326442 chr12 133851895 1194437 0.008923571832882903 0.12874284729983357 chr13 115169878 963037 0.008361882609617769 0.11949869902616668 chr14 107349540 796179 0.0074166968950216275 0.11663637022979315 chr15 102531392 726079 0.007081528747800479 0.1268930622874258 chr16 90354753 697242 0.007716716352486736 0.12080711285120271 chr17 81195210 689707 0.008494429659089496 0.12837888954631382 chr18 78077248 787133 0.010081464449156814 0.2035499299325567 chr19 59128983 522383 0.00883463529213753 0.14466378023089754 chr20 63025520 509668 0.008086692501704072 0.11938710160442668 chr21 48129895 404666 0.008407788963595288 0.12462887448394985 chr22 51304566 292894 0.005708926570005484 0.0977596971521212 chrMT 16571 39199 2.3655180737432864 2.1241919738615973 chrX 155270560 1540039 0.0099184223976522 0.1357933346318238 chrY 59373566 82734 0.0013934483908209254 0.04982622721336751