BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068172.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 = 3,494,777 number of mapped reads = 3,299,879 (94.42%) number of supplementary alignments = 27,770 (0.79%) number of secondary alignments = 0 number of mapped bases = 212,015,309 bp number of sequenced bases = 211,921,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 404,172 duplication rate = 10.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7525 >>>>>>> ACTG content number of A's = 55,417,937 bp (26.15%) number of C's = 37,959,827 bp (17.91%) number of T's = 69,132,867 bp (32.62%) number of G's = 49,386,146 bp (23.3%) number of N's = 24,288 bp (0.01%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,200,885 number of insertions = 13,135 mapped reads with insertion percentage = 0.39% number of deletions = 53,929 mapped reads with deletion percentage = 1.62% homopolymer indels = 44.8% >>>>>>> Coverage mean coverageData = 0.0685X std coverageData = 0.6864X There is a 5.16% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 23541187 0.09444785696241054 1.4082034794994294 chr2 243199373 20840402 0.08569266336060825 1.0509050760479994 chr3 198022430 14248678 0.07195486895095672 0.33972434630993337 chr4 191154276 9590808 0.05017312822235794 0.3051757795059107 chr5 180915260 8328200 0.04603370660938165 0.27936048757865056 chr6 171115067 12896898 0.07536973935790237 0.4737389614775147 chr7 159138663 14811894 0.09307539551215156 1.0105453442923569 chr8 146364022 9399807 0.06422211463962094 0.7466779644438754 chr9 141213431 7768016 0.05500904513820644 0.512501224265577 chr10 135534747 10495352 0.07743661483353785 0.5351076666318347 chr11 135006516 9970581 0.07385259093716633 0.47553410394424533 chr12 133851895 9563722 0.07145003064767966 0.3727644201148519 chr13 115169878 4683429 0.040665398638348824 0.28942594987330855 chr14 107349540 5615526 0.0523106666316409 0.349053349838796 chr15 102531392 5116801 0.04990472576437858 0.3125481965063738 chr16 90354753 4490653 0.0497002410044771 0.3117959777515922 chr17 81195210 5734187 0.0706222325183961 0.36737879318380073 chr18 78077248 4259449 0.05455429217997028 0.9372209061037426 chr19 59128983 3782476 0.06396991472016354 0.9154188471959676 chr20 63025520 3748450 0.05947511420770507 0.33236756374614 chr21 48129895 3616771 0.07514603969113168 0.3609751790789355 chr22 51304566 1667934 0.03251043971407925 0.22352414051568384 chrMT 16571 149186 9.002836280248626 5.806902446106615 chrX 155270560 17145132 0.11042100962345985 0.5054560041826761 chrY 59373566 549770 0.009259507842260982 0.25866786145551335