BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714150.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 704,348 number of mapped reads = 615,467 (87.38%) number of supplementary alignments = 18,060 (2.56%) number of secondary alignments = 0 number of mapped bases = 80,638,079 bp number of sequenced bases = 78,928,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 556,915 duplication rate = 44.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6318 >>>>>>> ACTG content number of A's = 21,109,233 bp (26.74%) number of C's = 17,721,737 bp (22.45%) number of T's = 20,080,009 bp (25.44%) number of G's = 20,017,005 bp (25.36%) number of N's = 509 bp (0%) GC percentage = 47.81% >>>>>>> Mismatches and indels general error rate = 0.0431 number of mismatches = 3,165,026 number of insertions = 85,169 mapped reads with insertion percentage = 13.38% number of deletions = 274,711 mapped reads with deletion percentage = 42.46% homopolymer indels = 30.32% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 7.4035X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8452598 0.03391204389416547 9.148965579801082 chr2 243199373 9574250 0.03936790577169786 12.535248149121509 chr3 198022430 2412341 0.01218216037445859 2.05263929744019 chr4 191154276 2282629 0.01194129185998434 2.493786976969272 chr5 180915260 4204123 0.02323807842411967 6.503147568020257 chr6 171115067 3237554 0.01892033271389246 4.081488758806649 chr7 159138663 2344853 0.014734653137056958 2.632901390869421 chr8 146364022 3014348 0.020594869960597284 4.70949931757128 chr9 141213431 3303044 0.023390437981780924 5.754213196308797 chr10 135534747 3685294 0.02719076902102455 4.982425827334158 chr11 135006516 3658094 0.02709568477420749 4.686388419262552 chr12 133851895 3666334 0.027390975675017526 4.909600058070308 chr13 115169878 3121086 0.02709984636781503 10.825724158440643 chr14 107349540 4367427 0.040684170607531246 20.941432164240304 chr15 102531392 2591567 0.02527583942291547 4.271770925313903 chr16 90354753 1549426 0.017148251182757368 2.482747646712987 chr17 81195210 3003696 0.0369935123020188 7.781139537784528 chr18 78077248 2152895 0.02757390987961051 5.359257874340938 chr19 59128983 2643573 0.044708582253139714 5.345318855501785 chr20 63025520 1923952 0.03052655495742042 4.977185778274948 chr21 48129895 630488 0.01309971692229954 2.063394721125138 chr22 51304566 457386 0.00891511293556211 1.1390819415599556 chrMT 16571 386743 23.338543238187196 203.8454723970444 chrX 155270560 7393653 0.04761786780443118 5.5421930033900715 chrY 59373566 580725 0.00978086780234827 2.416242392389926