BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472631.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,559,254 number of mapped reads = 17,400,065 (99.09%) number of supplementary alignments = 80,443 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,721,067 number of mapped paired reads (second in pair) = 8,678,998 number of mapped paired reads (both in pair) = 17,300,688 number of mapped paired reads (singletons) = 99,377 number of mapped bases = 1,708,699,213 bp number of sequenced bases = 1,708,488,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,046,056 duplication rate = 50.35% >>>>>>> Insert size mean insert size = 20,519.067 std insert size = 1,410,958.9068 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.7663 >>>>>>> ACTG content number of A's = 446,689,331 bp (26.15%) number of C's = 410,352,238 bp (24.02%) number of T's = 446,612,099 bp (26.14%) number of G's = 404,517,012 bp (23.68%) number of N's = 317,760 bp (0.02%) GC percentage = 47.7% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,603,571 number of insertions = 103,602 mapped reads with insertion percentage = 0.59% number of deletions = 87,539 mapped reads with deletion percentage = 0.5% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.552X std coverageData = 22.2472X There is a 3.47% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 262319148 1.0524312715754478 37.9959377307761 chr2 243199373 89162577 0.36662338352327906 14.923866872562941 chr3 198022430 113922190 0.5752994244136889 19.256617280035883 chr4 191154276 35667533 0.1865902963112371 11.375206359966121 chr5 180915260 61369841 0.3392187093559714 13.884855985572797 chr6 171115067 130563975 0.7630185774347972 25.003648255155337 chr7 159138663 102719354 0.6454707615584279 24.884582156242864 chr8 146364022 108673675 0.7424889909078886 25.14261724119929 chr9 141213431 92615208 0.6558526858539397 18.513612837969905 chr10 135534747 29084626 0.2145916574441239 10.267731115860839 chr11 135006516 44784022 0.33171748539900103 17.24025002671037 chr12 133851895 64413812 0.48123197658128036 15.217922982800305 chr13 115169878 46232667 0.4014301986149538 15.143530444494528 chr14 107349540 39873597 0.3714370550633007 27.73445059966497 chr15 102531392 24647075 0.2403856469636148 9.946442661223402 chr16 90354753 76566753 0.8474014975172363 33.00560380785442 chr17 81195210 111968133 1.3789992414577166 34.14551633457515 chr18 78077248 9551026 0.12232790274575252 6.029346465073022 chr19 59128983 51191423 0.8657585570176304 22.0944909727447 chr20 63025520 72480153 1.1500127726038596 30.289321257361802 chr21 48129895 16452652 0.3418385184509544 27.746109707704417 chr22 51304566 23089000 0.4500379167031644 21.395028532950995 chrMT 16571 6744 0.4069760424838573 0.7509566434707589 chrX 155270560 99934455 0.6436149583024625 24.152088425718762 chrY 59373566 1409574 0.023740767061220476 1.3970205929623158