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Detailed information for vg0217953192:

Variant ID: vg0217953192 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17953192
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAAAAAAAAAGACCCTTTCTCAACTAACAAAACAAATGAGCTACAAGAGTACTAACTACGGTTCTATAATAATTGATGCTTTGGACAAGGTTGAGGT[C/T]
AAACTTTTATAACTTTGACCATAAATAACTTTAAAAATATTTGGTTTAAAGAAACTAAAACAACATTTATAGATTTATCTTTCAAAGCACTATAATAAAA

Reverse complement sequence

TTTTATTATAGTGCTTTGAAAGATAAATCTATAAATGTTGTTTTAGTTTCTTTAAACCAAATATTTTTAAAGTTATTTATGGTCAAAGTTATAAAAGTTT[G/A]
ACCTCAACCTTGTCCAAAGCATCAATTATTATAGAACCGTAGTTAGTACTCTTGTAGCTCATTTGTTTTGTTAGTTGAGAAAGGGTCTTTTTTTTTTCTT

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 63.10% 36.50% 0.38% 0.06% NA
All Indica  2759 45.70% 53.70% 0.51% 0.07% NA
All Japonica  1512 97.20% 2.80% 0.00% 0.00% NA
Aus  269 36.40% 63.20% 0.37% 0.00% NA
Indica I  595 19.50% 80.50% 0.00% 0.00% NA
Indica II  465 25.20% 74.00% 0.86% 0.00% NA
Indica III  913 79.70% 19.90% 0.33% 0.00% NA
Indica Intermediate  786 38.20% 60.70% 0.89% 0.25% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 64.40% 31.10% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0217953192 C -> T LOC_Os02g30190.1 downstream_gene_variant ; 2251.0bp to feature; MODIFIER silent_mutation Average:29.025; most accessible tissue: Callus, score: 56.286 N N N N
vg0217953192 C -> T LOC_Os02g30200.1 intron_variant ; MODIFIER silent_mutation Average:29.025; most accessible tissue: Callus, score: 56.286 N N N N
vg0217953192 C -> DEL N N silent_mutation Average:29.025; most accessible tissue: Callus, score: 56.286 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217953192 NA 6.40E-08 mr1138 Ind_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
vg0217953192 NA 2.37E-07 mr1169 Ind_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
vg0217953192 NA 6.94E-06 mr1317 Ind_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
vg0217953192 NA 1.21E-06 mr1646 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
vg0217953192 9.70E-07 NA mr1855 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
vg0217953192 NA 6.03E-12 mr1138_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
vg0217953192 NA 2.06E-06 mr1138_2 Ind_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
vg0217953192 9.56E-06 NA mr1169_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
vg0217953192 2.36E-06 3.19E-07 mr1169_2 Ind_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
vg0217953192 NA 4.73E-07 mr1317_2 Ind_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
vg0217953192 NA 3.01E-07 mr1559_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
vg0217953192 NA 3.46E-10 mr1806_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
vg0217953192 NA 1.28E-08 mr1806_2 Ind_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
vg0217953192 NA 4.26E-07 mr1807_2 Ind_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
vg0217953192 NA 9.20E-07 mr1818_2 Ind_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
vg0217953192 1.53E-08 NA mr1855_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
vg0217953192 NA 1.76E-06 mr1870_2 Ind_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