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Detailed information for vg0615245465:

Variant ID: vg0615245465 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15245465
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTTGAATGTTTTATTATCTGGACTTTATGGAGATGTTGGCGGTATAGAATCAGCATTTAACAGCCGCCAACAAAACCCTCCACACTTAGCTCTTTGCT[T/C]
GTCCCTGAGTAAAGGTTAGTGTAGAATGAATTCCTTCAAGATACGAATCAAGCATATAAATCATTCACAACCATACCTGCACCTGTGAACTTTATCAGTG

Reverse complement sequence

CACTGATAAAGTTCACAGGTGCAGGTATGGTTGTGAATGATTTATATGCTTGATTCGTATCTTGAAGGAATTCATTCTACACTAACCTTTACTCAGGGAC[A/G]
AGCAAAGAGCTAAGTGTGGAGGGTTTTGTTGGCGGCTGTTAAATGCTGATTCTATACCGCCAACATCTCCATAAAGTCCAGATAATAAAACATTCAACAT

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 44.90% 41.30% 9.94% 3.87% NA
All Indica  2759 25.30% 53.00% 15.84% 5.84% NA
All Japonica  1512 91.00% 7.80% 0.86% 0.33% NA
Aus  269 2.60% 85.90% 5.58% 5.95% NA
Indica I  595 6.10% 85.90% 6.72% 1.34% NA
Indica II  465 11.60% 75.70% 8.17% 4.52% NA
Indica III  913 48.40% 15.80% 26.94% 8.87% NA
Indica Intermediate  786 21.20% 57.90% 14.38% 6.49% NA
Temperate Japonica  767 96.60% 1.80% 1.17% 0.39% NA
Tropical Japonica  504 82.10% 17.10% 0.60% 0.20% NA
Japonica Intermediate  241 91.70% 7.50% 0.41% 0.41% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 44.40% 48.90% 5.56% 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
vg0615245465 T -> C LOC_Os06g26050.1 upstream_gene_variant ; 2698.0bp to feature; MODIFIER silent_mutation Average:19.555; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg0615245465 T -> C LOC_Os06g26060.1 upstream_gene_variant ; 3469.0bp to feature; MODIFIER silent_mutation Average:19.555; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg0615245465 T -> C LOC_Os06g26040.1 downstream_gene_variant ; 4154.0bp to feature; MODIFIER silent_mutation Average:19.555; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg0615245465 T -> C LOC_Os06g26050-LOC_Os06g26060 intergenic_region ; MODIFIER silent_mutation Average:19.555; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N
vg0615245465 T -> DEL N N silent_mutation Average:19.555; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615245465 3.16E-07 NA mr1033 Jap_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
vg0615245465 6.03E-06 1.42E-07 mr1071 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
vg0615245465 1.44E-06 3.21E-09 mr1080 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
vg0615245465 NA 1.03E-07 mr1087 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
vg0615245465 NA 1.65E-06 mr1100 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
vg0615245465 NA 4.07E-07 mr1140 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
vg0615245465 NA 4.39E-10 mr1191 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
vg0615245465 NA 8.53E-09 mr1203 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
vg0615245465 4.37E-07 5.44E-10 mr1395 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
vg0615245465 6.21E-06 6.21E-06 mr1419 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
vg0615245465 1.86E-07 1.33E-09 mr1618 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
vg0615245465 4.22E-06 7.47E-09 mr1619 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
vg0615245465 NA 4.82E-10 mr1644 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
vg0615245465 NA 4.99E-23 mr1888 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
vg0615245465 NA 2.73E-06 mr1888 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
vg0615245465 NA 1.10E-06 mr1275_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
vg0615245465 NA 1.01E-10 mr1986_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