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Detailed information for vg0407668419:

Variant ID: vg0407668419 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7668419
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AGGATGTTAAGTGATAAAGTATCAGAATGTTTAGCTGATTACAAAAGTTCTAAGTCCTATTACATTAAGATTACTGTGATAAGTATTGCTGGATAGCCGA[T/C]
ATAGCTTTCTGCCTAATATGCTCTACTTCCTCTATGGCTTGAGCATCTTGAGCATCGGTTCCAGGAATAACTTTTAAGGACTTGGTCAGTTCAGCAACAT

Reverse complement sequence

ATGTTGCTGAACTGACCAAGTCCTTAAAAGTTATTCCTGGAACCGATGCTCAAGATGCTCAAGCCATAGAGGAAGTAGAGCATATTAGGCAGAAAGCTAT[A/G]
TCGGCTATCCAGCAATACTTATCACAGTAATCTTAATGTAATAGGACTTAGAACTTTTGTAATCAGCTAAACATTCTGATACTTTATCACTTAACATCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.00%	2.00%	9.33%	6.69%	NA
All Indica	2759	73.00%	3.40%	14.43%	9.13%	NA
All Japonica	1512	99.30%	0.00%	0.26%	0.40%	NA
Aus	269	71.70%	0.00%	10.04%	18.22%	NA
Indica I	595	82.20%	1.30%	8.24%	8.24%	NA
Indica II	465	68.20%	7.50%	16.99%	7.31%	NA
Indica III	913	69.90%	2.70%	16.32%	11.06%	NA
Indica Intermediate	786	72.50%	3.40%	15.39%	8.65%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.60%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	81.10%	1.10%	11.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407668419	T -> C	LOC_Os04g13750.1	3_prime_UTR_variant ; 628.0bp to feature; MODIFIER	silent_mutation	Average:7.957; most accessible tissue: Callus, score: 23.614	N	N	N	N
vg0407668419	T -> C	LOC_Os04g13740.1	downstream_gene_variant ; 1031.0bp to feature; MODIFIER	silent_mutation	Average:7.957; most accessible tissue: Callus, score: 23.614	N	N	N	N
vg0407668419	T -> DEL	N	N	silent_mutation	Average:7.957; most accessible tissue: Callus, score: 23.614	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407668419	NA	5.40E-07	mr1053	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
vg0407668419	NA	1.75E-07	mr1027_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
vg0407668419	NA	1.35E-07	mr1045_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
vg0407668419	3.11E-06	4.63E-10	mr1053_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
vg0407668419	NA	2.16E-06	mr1053_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
vg0407668419	9.97E-06	NA	mr1147_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
vg0407668419	NA	7.86E-06	mr1204_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
vg0407668419	NA	6.50E-06	mr1204_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
vg0407668419	3.87E-06	7.06E-08	mr1250_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