BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971311.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,287,431 number of mapped reads = 8,641,374 (93.04%) number of supplementary alignments = 1,353 (0.01%) number of secondary alignments = 0 number of mapped bases = 414,104,131 bp number of sequenced bases = 414,014,546 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,201 duplication rate = 6.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.9743 >>>>>>> ACTG content number of A's = 115,617,792 bp (27.93%) number of C's = 88,693,388 bp (21.42%) number of T's = 117,606,785 bp (28.41%) number of G's = 92,075,558 bp (22.24%) number of N's = 21,023 bp (0.01%) GC percentage = 43.66% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 2,158,654 number of insertions = 28,692 mapped reads with insertion percentage = 0.33% number of deletions = 62,077 mapped reads with deletion percentage = 0.72% homopolymer indels = 40% >>>>>>> Coverage mean coverageData = 0.1338X std coverageData = 1.0456X There is a 9.4% of reference with a coverageData >= 1X There is a 2.5% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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% 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 33568899 0.13467929935468445 1.4977285565110892 chr2 243199373 37468462 0.15406479686935706 1.0861218179118293 chr3 198022430 26966829 0.13618067912811696 0.49845286896907776 chr4 191154276 28936301 0.151376686964617 0.8456100204432043 chr5 180915260 22911969 0.12664475622454402 0.4851500097652948 chr6 171115067 21899931 0.12798365090784203 0.5057408960034895 chr7 159138663 25185326 0.1582602588536263 1.6412473213150462 chr8 146364022 20915763 0.14290235205479662 2.0863631318839895 chr9 141213431 16193708 0.11467540931003936 0.9522548667278493 chr10 135534747 22090750 0.16298956901435763 1.389529395794068 chr11 135006516 17123903 0.1268376038975778 0.7787861614809575 chr12 133851895 20480976 0.15301222294985065 0.5488023226253141 chr13 115169878 13898299 0.12067651057162707 0.46420274079749796 chr14 107349540 12788395 0.11912854959602062 0.651961444883513 chr15 102531392 11801369 0.11510005638078141 0.4676260039537658 chr16 90354753 11592275 0.12829734590719316 0.6344576230291161 chr17 81195210 10060699 0.12390754331443936 0.5745644710472064 chr18 78077248 11942200 0.1529536491859959 1.8890959104409226 chr19 59128983 9528412 0.16114621825983377 1.3496627542490112 chr20 63025520 7885880 0.12512201406668283 0.5576026102044374 chr21 48129895 5333793 0.1108207902801367 0.8051082212449387 chr22 51304566 4759504 0.09276959871368953 0.5129910458807888 chrMT 16571 26690 1.610645102890592 1.7788562226183562 chrX 155270560 16718647 0.10767428802987508 0.5497000880008288 chrY 59373566 4025151 0.06779365416589599 0.7494856778979855