BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818840.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,847,684 number of mapped reads = 1,824,056 (98.72%) number of supplementary alignments = 28,867 (1.56%) number of secondary alignments = 0 number of mapped bases = 168,807,804 bp number of sequenced bases = 168,698,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 435,170 duplication rate = 20.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3549 >>>>>>> ACTG content number of A's = 48,044,280 bp (28.48%) number of C's = 35,563,311 bp (21.08%) number of T's = 48,470,762 bp (28.73%) number of G's = 36,618,039 bp (21.71%) number of N's = 2,289 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 998,405 number of insertions = 26,104 mapped reads with insertion percentage = 1.37% number of deletions = 54,035 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 0.6844X There is a 3.68% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 16754314 0.06721874526443006 0.8485113294913685 chr2 243199373 12920023 0.05312523153585597 1.2718460344112823 chr3 198022430 10188043 0.05144893434546784 0.3114101467815877 chr4 191154276 7953849 0.041609579269887745 0.3945263966685785 chr5 180915260 7393840 0.040869078705687956 0.32299982798245097 chr6 171115067 8307447 0.04854889254141484 0.34729052004135463 chr7 159138663 14613948 0.09183153687799929 1.3079332902772989 chr8 146364022 13914189 0.09506563710035243 0.5306403138154768 chr9 141213431 6286749 0.04451948341939231 0.5007460714942666 chr10 135534747 7891129 0.05822218416064184 0.8768974723497348 chr11 135006516 7586357 0.05619252481117282 0.3864990529785206 chr12 133851895 6823877 0.0509808023263324 0.3157667302914245 chr13 115169878 4851777 0.04212713501354929 0.2796567838161871 chr14 107349540 5166360 0.04812652201397416 0.34314018085593173 chr15 102531392 4876573 0.047561755525566254 0.29643258786689825 chr16 90354753 4488183 0.04967290431306918 0.9552845321305515 chr17 81195210 4978130 0.06131063642793707 0.4085155467882277 chr18 78077248 3030556 0.03881484142473874 0.5360624144873982 chr19 59128983 3217669 0.054417797106369986 0.8098775584182837 chr20 63025520 7276766 0.11545745279055214 0.5142005974391135 chr21 48129895 1618152 0.03362051797536646 0.2797107020062103 chr22 51304566 1813076 0.03533946666657311 0.3181898402579749 chrMT 16571 142338 8.589584213384828 6.1497463957940095 chrX 155270560 6128579 0.03947032199793702 0.33178386479141586 chrY 59373566 585880 0.009867690951896 1.0739033922899426