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Detailed information for vg0223585784:

Variant ID: vg0223585784 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23585784
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: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GACGCAACAGATATATTATATGTTGCAGAGCGACAGTCATATTATGCAATTTTTAAGCCGCCATCATTCAAATATATTTGTAATGGATCAATGTGGAAGG[T/C]
CATTGTGGCAGTGTGCCCATCCTGTTGTTTTGCGATGAGTAATAGTTTTACCTTGTGCACTTTTTCAACAGCAATAGTTTTCATCATATTGTTTGTAAAA

Reverse complement sequence

TTTTACAAACAATATGATGAAAACTATTGCTGTTGAAAAAGTGCACAAGGTAAAACTATTACTCATCGCAAAACAACAGGATGGGCACACTGCCACAATG[A/G]
CCTTCCACATTGATCCATTACAAATATATTTGAATGATGGCGGCTTAAAAATTGCATAATATGACTGTCGCTCTGCAACATATAATATATCTGTTGCGTC

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	61.30%	38.40%	0.25%	0.00%	NA
All Indica	2759	39.90%	59.80%	0.36%	0.00%	NA
All Japonica	1512	96.60%	3.40%	0.07%	0.00%	NA
Aus	269	69.90%	30.10%	0.00%	0.00%	NA
Indica I	595	48.20%	50.90%	0.84%	0.00%	NA
Indica II	465	41.50%	58.30%	0.22%	0.00%	NA
Indica III	913	33.50%	66.50%	0.00%	0.00%	NA
Indica Intermediate	786	39.90%	59.50%	0.51%	0.00%	NA
Temperate Japonica	767	98.70%	1.20%	0.13%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	11.50%	1.04%	0.00%	NA
Intermediate	90	72.20%	27.80%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223585784	T -> C	LOC_Os02g39050.1	upstream_gene_variant ; 4937.0bp to feature; MODIFIER	silent_mutation	Average:46.506; most accessible tissue: Callus, score: 78.409	N	N	N	N
vg0223585784	T -> C	LOC_Os02g39060.1	downstream_gene_variant ; 1958.0bp to feature; MODIFIER	silent_mutation	Average:46.506; most accessible tissue: Callus, score: 78.409	N	N	N	N
vg0223585784	T -> C	LOC_Os02g39064.1	intron_variant ; MODIFIER	silent_mutation	Average:46.506; most accessible tissue: Callus, score: 78.409	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223585784	NA	5.04E-07	mr1746	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
vg0223585784	NA	5.60E-07	mr1227_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
vg0223585784	NA	7.80E-06	mr1594_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
vg0223585784	9.05E-07	NA	mr1746_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
vg0223585784	8.05E-07	2.22E-12	mr1746_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
vg0223585784	NA	1.73E-06	mr1863_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