BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104296.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 1,522,045,848 number of mapped reads = 1,381,813,333 (90.79%) number of supplementary alignments = 11,244 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 694,910,726 number of mapped paired reads (second in pair) = 686,902,607 number of mapped paired reads (both in pair) = 1,368,605,890 number of mapped paired reads (singletons) = 13,207,443 number of mapped bases = 68,083,098,079 bp number of sequenced bases = 68,074,584,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 960,268,593 duplication rate = 40.83% >>>>>>> Insert size mean insert size = 7,105.4455 std insert size = 892,103.0854 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.8317 >>>>>>> ACTG content number of A's = 16,555,511,990 bp (24.32%) number of C's = 17,525,025,539 bp (25.74%) number of T's = 16,577,645,807 bp (24.35%) number of G's = 17,414,978,269 bp (25.58%) number of N's = 1,422,691 bp (0%) GC percentage = 51.33% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 191,275,503 number of insertions = 4,045,231 mapped reads with insertion percentage = 0.29% number of deletions = 4,844,105 mapped reads with deletion percentage = 0.35% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 21.9928X std coverageData = 721.0528X There is a 86.53% of reference with a coverageData >= 1X There is a 80.32% of reference with a coverageData >= 2X There is a 73.62% of reference with a coverageData >= 3X There is a 66.92% of reference with a coverageData >= 4X There is a 60.46% of reference with a coverageData >= 5X There is a 54.44% of reference with a coverageData >= 6X There is a 48.91% of reference with a coverageData >= 7X There is a 43.93% of reference with a coverageData >= 8X There is a 39.47% of reference with a coverageData >= 9X There is a 35.51% of reference with a coverageData >= 10X There is a 32.01% of reference with a coverageData >= 11X There is a 28.93% of reference with a coverageData >= 12X There is a 26.22% of reference with a coverageData >= 13X There is a 23.83% of reference with a coverageData >= 14X There is a 21.74% of reference with a coverageData >= 15X There is a 19.9% of reference with a coverageData >= 16X There is a 18.27% of reference with a coverageData >= 17X There is a 16.84% of reference with a coverageData >= 18X There is a 15.58% of reference with a coverageData >= 19X There is a 14.46% of reference with a coverageData >= 20X There is a 13.46% of reference with a coverageData >= 21X There is a 12.58% of reference with a coverageData >= 22X There is a 11.79% of reference with a coverageData >= 23X There is a 11.09% of reference with a coverageData >= 24X There is a 10.46% of reference with a coverageData >= 25X There is a 9.89% of reference with a coverageData >= 26X There is a 9.37% of reference with a coverageData >= 27X There is a 8.91% of reference with a coverageData >= 28X There is a 8.49% of reference with a coverageData >= 29X There is a 8.1% of reference with a coverageData >= 30X There is a 7.76% of reference with a coverageData >= 31X There is a 7.44% of reference with a coverageData >= 32X There is a 7.14% of reference with a coverageData >= 33X There is a 6.87% of reference with a coverageData >= 34X There is a 6.63% of reference with a coverageData >= 35X There is a 6.4% of reference with a coverageData >= 36X There is a 6.18% of reference with a coverageData >= 37X There is a 5.99% of reference with a coverageData >= 38X There is a 5.8% of reference with a coverageData >= 39X There is a 5.63% of reference with a coverageData >= 40X There is a 5.47% of reference with a coverageData >= 41X There is a 5.32% of reference with a coverageData >= 42X There is a 5.18% of reference with a coverageData >= 43X There is a 5.05% of reference with a coverageData >= 44X There is a 4.92% of reference with a coverageData >= 45X There is a 4.81% of reference with a coverageData >= 46X There is a 4.7% of reference with a coverageData >= 47X There is a 4.59% of reference with a coverageData >= 48X There is a 4.49% of reference with a coverageData >= 49X There is a 4.4% of reference with a coverageData >= 50X There is a 4.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6232794635 25.00613482924883 469.6661498802163 chr2 243199373 4870206371 20.02557124602455 150.33702609709246 chr3 198022430 3913247886 19.76163955770061 115.17396437820881 chr4 191154276 2836113181 14.83677603424367 89.24281395961124 chr5 180915260 3383916665 18.704429162028674 147.82708825360893 chr6 171115067 3607614681 21.08297500768883 116.85456960299877 chr7 159138663 3237653762 20.344859639797274 138.8973871513562 chr8 146364022 2632094786 17.983208920017244 106.49502316035716 chr9 141213431 2662186715 18.852220331648198 117.6908140486458 chr10 135534747 2841058327 20.96184476590346 114.62538425008711 chr11 135006516 3197710606 23.685602004572875 165.51439917699778 chr12 133851895 3086559525 23.05951309094279 132.07473369245562 chr13 115169878 1484338698 12.888254496544661 161.74489492116945 chr14 107349540 2054268665 19.13625959645472 122.7983220332526 chr15 102531392 2400260203 23.4100030847138 139.57488499477978 chr16 90354753 2360380371 26.123477654794762 151.24889229213488 chr17 81195210 2935921073 36.15879647333876 223.42351919364572 chr18 78077248 1260008317 16.137970398239446 96.88334173490202 chr19 59128983 2799983212 47.35381990250027 244.15081616138318 chr20 63025520 1560258244 24.755975738081972 132.7293868752368 chr21 48129895 708729047 14.725339562864203 106.97145502253227 chr22 51304566 1274634282 24.844460861436776 143.6119949270631 chrMT 16571 4831515505 291564.5105907911 75714.24593418051 chrX 155270560 1840862755 11.85583896264688 66.62145558714597 chrY 59373566 70780567 1.192122551641921 41.72109183919141