BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524884.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,702,931 number of mapped reads = 1,573,065 (92.37%) number of supplementary alignments = 5,409 (0.32%) number of secondary alignments = 0 number of mapped bases = 92,003,105 bp number of sequenced bases = 91,975,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,140 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4054 >>>>>>> ACTG content number of A's = 23,954,912 bp (26.04%) number of C's = 15,342,975 bp (16.68%) number of T's = 29,763,182 bp (32.36%) number of G's = 22,902,122 bp (24.9%) number of N's = 11,903 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 449,350 number of insertions = 6,881 mapped reads with insertion percentage = 0.44% number of deletions = 17,696 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.2946X There is a 2.68% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7382592 0.029619151881671742 0.58441234215831 chr2 243199373 7910061 0.03252500572853039 0.31076132382179766 chr3 198022430 6185173 0.031234709118557934 0.19089341395663886 chr4 191154276 5944049 0.031095558647089853 0.21278885816021179 chr5 180915260 5409629 0.029901452204750444 0.1890810721127762 chr6 171115067 5328433 0.031139472948925065 0.20825842683550963 chr7 159138663 4892891 0.03074608588360454 0.3622516661418681 chr8 146364022 4598035 0.03141506319087077 0.29017461542328704 chr9 141213431 3844873 0.02722738887351303 0.2561914742520593 chr10 135534747 4439583 0.03275605037282432 0.2781305552969094 chr11 135006516 4231035 0.0313394873474107 0.2698891568325039 chr12 133851895 4207746 0.03143583436005893 0.19456391817522442 chr13 115169878 2913055 0.025293549412286433 0.1736536471500013 chr14 107349540 2839885 0.026454561426159814 0.18696592889845778 chr15 102531392 2634421 0.025693799221998274 0.17317103955660096 chr16 90354753 2659433 0.029433238559127044 0.2015745615663813 chr17 81195210 2396306 0.029512898605718242 0.2010791451841794 chr18 78077248 2554727 0.032720505210429546 0.528013614697545 chr19 59128983 1778079 0.03007119199056747 0.3823034191328134 chr20 63025520 1933018 0.03067040145007927 0.1942523167335559 chr21 48129895 1224251 0.025436394573476632 0.19241728572267194 chr22 51304566 1028431 0.02004560373827156 0.15296751887789892 chrMT 16571 6985 0.4215195220566049 0.7320637498210801 chrX 155270560 5376815 0.034628682990516683 0.23110466495153553 chrY 59373566 283599 0.004776519571015829 0.13486497762845104