BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083095.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,117,130 number of mapped reads = 3,579,785 (86.95%) number of supplementary alignments = 19,810 (0.48%) number of secondary alignments = 0 number of mapped bases = 238,116,447 bp number of sequenced bases = 238,025,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,841 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6708 >>>>>>> ACTG content number of A's = 65,807,099 bp (27.65%) number of C's = 43,014,893 bp (18.07%) number of T's = 76,850,193 bp (32.29%) number of G's = 52,329,890 bp (21.98%) number of N's = 23,447 bp (0.01%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,067,419 number of insertions = 19,637 mapped reads with insertion percentage = 0.54% number of deletions = 52,947 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.0769X std coverageData = 0.6073X There is a 5.87% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 22324805 0.0895677006156787 0.9849704076630513 chr2 243199373 24924178 0.10248454875745094 0.8182044713918357 chr3 198022430 16078062 0.08119313554530161 0.35761401070855175 chr4 191154276 12993802 0.06797547128896034 0.34246595243576583 chr5 180915260 13446130 0.07432280726346689 0.3458665300574094 chr6 171115067 16130786 0.09426864789177215 0.5193730733136566 chr7 159138663 11942140 0.07504235472934695 0.7419372201582711 chr8 146364022 21788744 0.14886680279939288 0.7609047087927927 chr9 141213431 7226824 0.051176605148840267 0.6458664523123735 chr10 135534747 8933444 0.06591257369595414 0.5087713868050187 chr11 135006516 10260828 0.07600246494769186 0.4803769685821274 chr12 133851895 7602959 0.05680128025083246 0.3177652312768569 chr13 115169878 5752218 0.0499455074529123 0.2798477622525267 chr14 107349540 4606099 0.042907487074467204 0.35497924029263667 chr15 102531392 3941852 0.03844531828847111 0.24442255094395174 chr16 90354753 8644581 0.09567378265092485 0.46298850415074 chr17 81195210 5539295 0.06822194314171981 0.36528890988577506 chr18 78077248 8487495 0.10870638012241415 1.406627205331982 chr19 59128983 3786647 0.06404045542268164 0.6993565929710203 chr20 63025520 4703143 0.07462283532131112 0.3662446118724892 chr21 48129895 4782597 0.09936853176180833 0.41052885633877456 chr22 51304566 3441641 0.06708254777947055 0.3230626251096322 chrMT 16571 435990 26.310421821253996 20.078368100401512 chrX 155270560 9920390 0.06389099131219723 0.40227321670876853 chrY 59373566 421797 0.007104121049424587 0.1469513444878679