BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013346.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 = 1,898,958 number of mapped reads = 1,685,291 (88.75%) number of supplementary alignments = 11,458 (0.6%) number of secondary alignments = 0 number of mapped bases = 112,019,074 bp number of sequenced bases = 111,967,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,985 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9581 >>>>>>> ACTG content number of A's = 30,227,465 bp (27%) number of C's = 21,491,529 bp (19.19%) number of T's = 34,617,247 bp (30.92%) number of G's = 25,602,242 bp (22.87%) number of N's = 28,954 bp (0.03%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 892,016 number of insertions = 7,587 mapped reads with insertion percentage = 0.45% number of deletions = 29,386 mapped reads with deletion percentage = 1.72% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3045X There is a 2.97% of reference with a coverageData >= 1X There is a 0.47% 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% 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 8287576 0.03324997132103434 0.43232067607759295 chr2 243199373 11250044 0.04625852386552 0.3899406987560587 chr3 198022430 7019522 0.035448115650333144 0.2207252936353897 chr4 191154276 6862221 0.03589886213165328 0.22698557270213174 chr5 180915260 6081198 0.03361351607376846 0.21618564156580297 chr6 171115067 6091607 0.0355994776310376 0.26250366745160175 chr7 159138663 6820679 0.042859974260309075 0.4868221483529859 chr8 146364022 6035519 0.04123635656855617 0.2956896375652184 chr9 141213431 4102072 0.029048738288923806 0.25801921159259167 chr10 135534747 5241102 0.03866980324978952 0.3186845191540813 chr11 135006516 4795735 0.035522248422439104 0.2557866740318219 chr12 133851895 5487079 0.04099365944725698 0.2394632522348502 chr13 115169878 2888650 0.025081645046111798 0.18952297357810574 chr14 107349540 3673620 0.034221106117455186 0.2273295956520432 chr15 102531392 3204073 0.03124967814735218 0.20875391463637932 chr16 90354753 3755244 0.04156111189856277 0.25773854410278796 chr17 81195210 3026647 0.03727617675968816 0.24658818554011647 chr18 78077248 2711484 0.034728221978315627 0.3992236290940111 chr19 59128983 2410486 0.04076657296811616 0.36919417975380087 chr20 63025520 2610237 0.0414155567459023 0.24291682114099153 chr21 48129895 1897594 0.03942651443557066 0.2443544662650498 chr22 51304566 1238518 0.024140502426236294 0.1834177855493092 chrMT 16571 338752 20.44245971878583 13.101542925930875 chrX 155270560 5955114 0.03835314305557989 0.24427068178103412 chrY 59373566 234301 0.003946217412644543 0.09227266576651288