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Detailed information for vg0320115825:

Variant ID: vg0320115825 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20115825
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, C: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

GGGAGAGGCAGAGATGGAGCTCGGCGTTTTTAGGGCGTCGACACGTCGTGGCCACGCGTCGCGCAGCGTCCAGAGCCGGTCGGCGCTCGATCTCTCCCTC[T/C]
CAGTGTTTCTCAGTCGGCTAGGGAAGTTGCACACAGGAAGGGCAAACCGGAGGGATTGACAAGGGGGCCCAGGTCGAAGTAAACTAGGTGGAAGAGAGAT

Reverse complement sequence

ATCTCTCTTCCACCTAGTTTACTTCGACCTGGGCCCCCTTGTCAATCCCTCCGGTTTGCCCTTCCTGTGTGCAACTTCCCTAGCCGACTGAGAAACACTG[A/G]
GAGGGAGAGATCGAGCGCCGACCGGCTCTGGACGCTGCGCGACGCGTGGCCACGACGTGTCGACGCCCTAAAAACGCCGAGCTCCATCTCTGCCTCTCCC

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	84.60%	11.30%	1.33%	2.81%	NA
All Indica	2759	80.60%	13.00%	2.21%	4.13%	NA
All Japonica	1512	87.60%	11.10%	0.07%	1.19%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.50%	4.00%	0.84%	0.67%	NA
Indica II	465	76.60%	17.20%	2.58%	3.66%	NA
Indica III	913	70.30%	18.40%	3.83%	7.45%	NA
Indica Intermediate	786	84.50%	11.20%	1.15%	3.18%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	69.40%	30.20%	0.20%	0.20%	NA
Japonica Intermediate	241	86.30%	6.60%	0.00%	7.05%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	1.11%	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
vg0320115825	T -> C	LOC_Os03g36270.1	upstream_gene_variant ; 4658.0bp to feature; MODIFIER	silent_mutation	Average:43.289; most accessible tissue: Callus, score: 96.655	N	N	N	N
vg0320115825	T -> C	LOC_Os03g36260.1	downstream_gene_variant ; 4833.0bp to feature; MODIFIER	silent_mutation	Average:43.289; most accessible tissue: Callus, score: 96.655	N	N	N	N
vg0320115825	T -> C	LOC_Os03g36260-LOC_Os03g36270	intergenic_region ; MODIFIER	silent_mutation	Average:43.289; most accessible tissue: Callus, score: 96.655	N	N	N	N
vg0320115825	T -> DEL	N	N	silent_mutation	Average:43.289; most accessible tissue: Callus, score: 96.655	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320115825	NA	1.93E-07	mr1217	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
vg0320115825	3.13E-10	2.46E-11	mr1439	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
vg0320115825	3.09E-07	5.48E-09	mr1439	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
vg0320115825	NA	4.32E-07	mr1845	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
vg0320115825	NA	1.40E-07	mr1852	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
vg0320115825	NA	9.33E-09	mr1852	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
vg0320115825	NA	5.80E-08	mr1136_2	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
vg0320115825	NA	1.48E-06	mr1439_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