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Detailed information for vg0420224800:

Variant ID: vg0420224800 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20224800
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GCTAAGGTTCAACCGTTTGCTGAAATAAGTTGTCCAATAACGGAGAATCACTATATAAAGCTTATACAGAACATAGTAACTGTAAGCACTGCGGTTCCAG[C/T]
TGATATATATCCTGTTTTCTAACAAGCGAAGAGGGTCGTCTGAATCAAATCAGCAACATCATAACTGGTGGCTCTCTTCACTCTCCTGGGGCAGAGACAC

Reverse complement sequence

GTGTCTCTGCCCCAGGAGAGTGAAGAGAGCCACCAGTTATGATGTTGCTGATTTGATTCAGACGACCCTCTTCGCTTGTTAGAAAACAGGATATATATCA[G/A]
CTGGAACCGCAGTGCTTACAGTTACTATGTTCTGTATAAGCTTTATATAGTGATTCTCCGTTATTGGACAACTTATTTCAGCAAACGGTTGAACCTTAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.60% 49.00% 0.04% 0.38% NA
All Indica  2759 83.10% 16.50% 0.04% 0.33% NA
All Japonica  1512 0.50% 99.20% 0.00% 0.26% NA
Aus  269 23.80% 76.20% 0.00% 0.00% NA
Indica I  595 98.50% 1.00% 0.00% 0.50% NA
Indica II  465 79.40% 20.00% 0.00% 0.65% NA
Indica III  913 76.60% 23.40% 0.00% 0.00% NA
Indica Intermediate  786 81.30% 18.20% 0.13% 0.38% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.60% 0.00% 0.40% NA
Japonica Intermediate  241 0.00% 99.20% 0.00% 0.83% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 26.70% 66.70% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420224800 C -> DEL N N silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33440.2 3_prime_UTR_variant ; 78.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33450.1 upstream_gene_variant ; 1726.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33450.3 upstream_gene_variant ; 1726.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33450.2 upstream_gene_variant ; 1718.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33430.1 downstream_gene_variant ; 2084.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N
vg0420224800 C -> T LOC_Os04g33420.1 downstream_gene_variant ; 4422.0bp to feature; MODIFIER silent_mutation Average:72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420224800 NA 8.36E-30 mr1208 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 6.34E-10 mr1299 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 7.78E-07 mr1321 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.93E-25 mr1551 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.39E-18 mr1552 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.09E-18 mr1598 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 8.51E-09 mr1648 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 6.14E-15 mr1655 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 2.70E-18 mr1700 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 8.55E-12 mr1713 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 4.12E-07 mr1717 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 6.06E-07 mr1756 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.34E-10 mr1770 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 3.69E-07 mr1804 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 3.53E-12 mr1914 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.92E-08 mr1946 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.49E-38 mr1208_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.39E-07 mr1321_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 6.37E-20 mr1362_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.93E-09 mr1398_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 4.92E-15 mr1578_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 2.06E-18 mr1581_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.20E-32 mr1598_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 2.83E-17 mr1712_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 1.14E-13 mr1717_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 5.00E-48 mr1721_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 6.01E-13 mr1770_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 2.30E-18 mr1836_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 3.51E-10 mr1946_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0420224800 NA 3.51E-10 mr1948_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251