BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240238.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 = 2,820,144 number of mapped reads = 2,053,235 (72.81%) number of supplementary alignments = 16,023 (0.57%) number of secondary alignments = 0 number of mapped bases = 135,988,310 bp number of sequenced bases = 135,925,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 317,254 duplication rate = 11.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9603 >>>>>>> ACTG content number of A's = 38,302,377 bp (28.18%) number of C's = 24,983,227 bp (18.38%) number of T's = 43,515,714 bp (32.01%) number of G's = 29,071,721 bp (21.39%) number of N's = 52,056 bp (0.04%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,178,765 number of insertions = 9,987 mapped reads with insertion percentage = 0.48% number of deletions = 36,151 mapped reads with deletion percentage = 1.74% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.5121X There is a 1.85% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 10677821 0.04283969667622212 0.7677875833665551 chr2 243199373 15219308 0.06257955278527795 0.613622343129532 chr3 198022430 8163503 0.04122514303051427 0.4021936723554854 chr4 191154276 8731625 0.045678418410059526 0.4300763520016917 chr5 180915260 7157408 0.03956221271771104 0.39257541405344504 chr6 171115067 7176447 0.04193930508761102 0.4285660597677404 chr7 159138663 8699901 0.05466868224222796 0.7082598909589173 chr8 146364022 7762697 0.05303692050769143 0.6732923080907296 chr9 141213431 4793069 0.03394201929701715 0.4276394488159492 chr10 135534747 6372002 0.04701378901751298 0.482284413146362 chr11 135006516 5614959 0.041590281464636863 0.4518911888213215 chr12 133851895 7085016 0.05293175714845128 0.45749925136959546 chr13 115169878 3577940 0.031066630113127325 0.35410325944941423 chr14 107349540 4474484 0.041681445491056596 0.41595237945901675 chr15 102531392 4218922 0.04114761262579952 0.410218648477606 chr16 90354753 3735652 0.04134427770501459 0.40038261903521793 chr17 81195210 3306334 0.040720801140855474 0.4110033916549939 chr18 78077248 3265491 0.0418238486069591 0.6953708000788329 chr19 59128983 2296967 0.03884671921382446 0.521893701814018 chr20 63025520 2674408 0.042433731605863785 0.4102805279787941 chr21 48129895 2190186 0.045505729858749955 0.4254622271712072 chr22 51304566 1340792 0.02613397022011647 0.30962297470665806 chrMT 16571 15378 0.9280067587954861 1.9430980937577276 chrX 155270560 7089644 0.04565993708015222 0.4353793160068378 chrY 59373566 348356 0.005867190122958085 0.13893607451584894