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Detailed information for vg0504291251:

Variant ID: vg0504291251 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 4291251
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGACTAGAGTTGGATATCAAATGGAGCACGCCCCACTTAGAGACAGAGTCGTAACTTTTCTTGCATTTGTCAAAGTTATTTCCATTTGCACCCTAGAC[T/C]
CTAACATATATCTTCTCACGCTTTCAGTCGAGAGAGCTCCTCAGGAGTGTGAATGAAATGGGGCATGCCCTCCAAGCTCCGAGGGGTGGTGAGGACACGG

Reverse complement sequence

CCGTGTCCTCACCACCCCTCGGAGCTTGGAGGGCATGCCCCATTTCATTCACACTCCTGAGGAGCTCTCTCGACTGAAAGCGTGAGAAGATATATGTTAG[A/G]
GTCTAGGGTGCAAATGGAAATAACTTTGACAAATGCAAGAAAAGTTACGACTCTGTCTCTAAGTGGGGCGTGCTCCATTTGATATCCAACTCTAGTCCGG

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 37.90% 29.90% 19.64% 12.55% NA
All Indica  2759 10.70% 49.10% 20.44% 19.68% NA
All Japonica  1512 89.90% 0.70% 7.94% 1.39% NA
Aus  269 4.10% 8.20% 82.16% 5.58% NA
Indica I  595 21.50% 61.50% 10.08% 6.89% NA
Indica II  465 7.30% 41.90% 22.80% 27.96% NA
Indica III  913 5.00% 49.20% 21.36% 24.42% NA
Indica Intermediate  786 11.20% 44.00% 25.83% 18.96% NA
Temperate Japonica  767 97.40% 1.30% 1.17% 0.13% NA
Tropical Japonica  504 77.00% 0.00% 19.64% 3.37% NA
Japonica Intermediate  241 93.40% 0.40% 4.98% 1.24% NA
VI/Aromatic  96 82.30% 2.10% 11.46% 4.17% NA
Intermediate  90 52.20% 23.30% 13.33% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0504291251 T -> DEL N N silent_mutation Average:15.47; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 N N N N
vg0504291251 T -> C LOC_Os05g07920.1 intron_variant ; MODIFIER silent_mutation Average:15.47; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0504291251 2.84E-06 NA mr1076 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
vg0504291251 1.61E-06 6.77E-06 mr1083 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
vg0504291251 1.50E-07 9.53E-07 mr1086 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
vg0504291251 7.32E-07 6.96E-07 mr1103 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
vg0504291251 8.45E-08 3.07E-07 mr1104 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
vg0504291251 7.43E-07 2.56E-07 mr1107 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
vg0504291251 1.87E-07 4.00E-07 mr1226 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
vg0504291251 4.98E-06 3.19E-07 mr1246 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
vg0504291251 1.46E-06 NA mr1411 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
vg0504291251 3.46E-06 1.42E-06 mr1560 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