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Detailed information for vg0521659473:

Variant ID: vg0521659473 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21659473
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.33, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTTTGAAAACCGAAGCCAGCAAAGCTAGTGTTATATTAAGTACGGGAGGAAAAAGTATTTACAAGATAACCAAAAGGAAGAAAGTACGAATTACCCC[T/C]
GAACTATCACGGTTATCCGAATTATTCCCCTGAATCACAAAACCGGACATTTTTCACACCCAATTATGTAAACCGGACGAATTACCCCTCTGATCCAATC

Reverse complement sequence

GATTGGATCAGAGGGGTAATTCGTCCGGTTTACATAATTGGGTGTGAAAAATGTCCGGTTTTGTGATTCAGGGGAATAATTCGGATAACCGTGATAGTTC[A/G]
GGGGTAATTCGTACTTTCTTCCTTTTGGTTATCTTGTAAATACTTTTTCCTCCCGTACTTAATATAACACTAGCTTTGCTGGCTTCGGTTTTCAAAAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.50% 35.50% 9.97% 6.03% NA
All Indica  2759 72.60% 1.40% 15.91% 10.00% NA
All Japonica  1512 1.10% 98.50% 0.26% 0.13% NA
Aus  269 83.60% 6.30% 8.18% 1.86% NA
Indica I  595 61.50% 0.50% 30.42% 7.56% NA
Indica II  465 73.80% 3.00% 12.47% 10.75% NA
Indica III  913 81.70% 0.70% 6.24% 11.39% NA
Indica Intermediate  786 69.80% 2.20% 18.19% 9.80% NA
Temperate Japonica  767 1.00% 98.70% 0.13% 0.13% NA
Tropical Japonica  504 0.80% 98.60% 0.40% 0.20% NA
Japonica Intermediate  241 1.70% 97.90% 0.41% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 46.70% 44.40% 6.67% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0521659473 T -> DEL N N silent_mutation Average:58.374; most accessible tissue: Callus, score: 75.961 N N N N
vg0521659473 T -> C LOC_Os05g37060.1 upstream_gene_variant ; 4093.0bp to feature; MODIFIER silent_mutation Average:58.374; most accessible tissue: Callus, score: 75.961 N N N N
vg0521659473 T -> C LOC_Os05g37070.1 downstream_gene_variant ; 1876.0bp to feature; MODIFIER silent_mutation Average:58.374; most accessible tissue: Callus, score: 75.961 N N N N
vg0521659473 T -> C LOC_Os05g37060-LOC_Os05g37070 intergenic_region ; MODIFIER silent_mutation Average:58.374; most accessible tissue: Callus, score: 75.961 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0521659473 NA 1.27E-12 mr1149 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
vg0521659473 5.15E-06 NA mr1265 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
vg0521659473 4.51E-06 NA mr1050_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0521659473 NA 1.30E-14 mr1162_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
vg0521659473 NA 7.73E-06 mr1184_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
vg0521659473 9.15E-07 1.17E-07 mr1329_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0521659473 6.61E-06 NA mr1337_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
vg0521659473 NA 3.10E-19 mr1342_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
vg0521659473 9.79E-06 2.65E-07 mr1524_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
vg0521659473 NA 1.95E-11 mr1595_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
vg0521659473 NA 1.60E-08 mr1600_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
vg0521659473 NA 1.73E-18 mr1637_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
vg0521659473 1.59E-06 NA mr1652_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0521659473 NA 1.01E-36 mr1689_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
vg0521659473 NA 2.27E-08 mr1690_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
vg0521659473 NA 1.97E-13 mr1713_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
vg0521659473 NA 3.71E-06 mr1754_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
vg0521659473 NA 6.21E-08 mr1783_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
vg0521659473 NA 1.30E-07 mr1804_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
vg0521659473 NA 5.84E-07 mr1819_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
vg0521659473 NA 6.70E-36 mr1888_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
vg0521659473 NA 1.02E-31 mr1891_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
vg0521659473 NA 2.35E-18 mr1945_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
vg0521659473 3.86E-06 1.20E-07 mr1982_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251