BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094143.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 440,338 number of mapped reads = 418,980 (95.15%) number of supplementary alignments = 17,158 (3.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 210,434 number of mapped paired reads (second in pair) = 208,546 number of mapped paired reads (both in pair) = 416,022 number of mapped paired reads (singletons) = 2,958 number of mapped bases = 55,021,968 bp number of sequenced bases = 53,374,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 391,187 duplication rate = 49.59% >>>>>>> Insert size mean insert size = 601,812.4565 std insert size = 6,906,074.7422 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 43.3599 >>>>>>> ACTG content number of A's = 14,517,181 bp (27.2%) number of C's = 12,159,235 bp (22.78%) number of T's = 13,939,509 bp (26.12%) number of G's = 12,758,169 bp (23.9%) number of N's = 582 bp (0%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.048 number of mismatches = 2,539,555 number of insertions = 31,865 mapped reads with insertion percentage = 7.41% number of deletions = 207,851 mapped reads with deletion percentage = 46.27% homopolymer indels = 28.78% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 3.5944X There is a 0.02% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 959797 0.003850730626665119 1.375310115757636 chr2 243199373 2016895 0.008293175163736956 2.370030135174303 chr3 198022430 1597990 0.008069742402413706 2.598261904924203 chr4 191154276 1149553 0.00601374462583301 1.832664303698667 chr5 180915260 518077 0.0028636445593367855 0.8996724154285727 chr6 171115067 1826270 0.010672759751775687 3.876801528427963 chr7 159138663 1340620 0.008424225607575954 2.409086266363494 chr8 146364022 1302725 0.008900582138963085 2.6614017826865726 chr9 141213431 623698 0.004416704527206056 1.5891530913371708 chr10 135534747 1054120 0.007777488971149221 2.1473447219083805 chr11 135006516 1322886 0.009798682605808448 2.552962725006037 chr12 133851895 1814216 0.013553905979440934 3.686345753552587 chr13 115169878 1174273 0.010196008022167045 2.198014500870164 chr14 107349540 347748 0.0032393990696187426 1.30914917983872 chr15 102531392 766766 0.007478353556343018 1.6611997018193794 chr16 90354753 394791 0.004369344023329907 1.1138222950193908 chr17 81195210 1457258 0.017947585824336188 4.120992610824172 chr18 78077248 235841 0.003020611074816571 0.848604043341574 chr19 59128983 417594 0.00706242486869764 1.9926501531121517 chr20 63025520 340683 0.005405477019467669 1.332197195256257 chr21 48129895 329423 0.006844457067691504 2.161954917327694 chr22 51304566 124927 0.0024350074416378455 0.5029710843750391 chrMT 16571 1570012 94.74455373845875 414.27505509143987 chrX 155270560 31888730 0.2053752494999696 11.762067544456237 chrY 59373566 447075 0.007529866068681137 1.7691451995355554