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Detailed information for vg0334773462:

Variant ID: vg0334773462 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34773462
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAACTTATGATTACTATTTTTATTGTTATTAGATGATAAAAATGTATGACTTTTTTTTTATTTTTTTTATAAATTTTTTAAATAAGACGGACGGTCAAA[T/C]
ATTGGACACGGATACTCACAGTTACACTTATTTTAGGACAGAGGTAGTACATCCGGTTTATAATAGCCGATTAACTTTTGAATACATGTTTAACCATTTA

Reverse complement sequence

TAAATGGTTAAACATGTATTCAAAAGTTAATCGGCTATTATAAACCGGATGTACTACCTCTGTCCTAAAATAAGTGTAACTGTGAGTATCCGTGTCCAAT[A/G]
TTTGACCGTCCGTCTTATTTAAAAAATTTATAAAAAAAATAAAAAAAAAGTCATACATTTTTATCATCTAATAACAATAAAAATAGTAATCATAAGTTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.90%	12.70%	2.35%	0.00%	NA
All Indica	2759	99.30%	0.50%	0.18%	0.00%	NA
All Japonica	1512	55.10%	38.40%	6.55%	0.00%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	0.80%	0.51%	0.00%	NA
Temperate Japonica	767	32.50%	58.10%	9.39%	0.00%	NA
Tropical Japonica	504	85.90%	11.90%	2.18%	0.00%	NA
Japonica Intermediate	241	62.70%	30.70%	6.64%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	3.33%	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
vg0334773462	T -> C	LOC_Os03g61220.1	downstream_gene_variant ; 1116.0bp to feature; MODIFIER	silent_mutation	Average:69.819; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0334773462	T -> C	LOC_Os03g61230.1	downstream_gene_variant ; 2503.0bp to feature; MODIFIER	silent_mutation	Average:69.819; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0334773462	T -> C	LOC_Os03g61220.2	downstream_gene_variant ; 1116.0bp to feature; MODIFIER	silent_mutation	Average:69.819; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0334773462	T -> C	LOC_Os03g61220-LOC_Os03g61230	intergenic_region ; MODIFIER	silent_mutation	Average:69.819; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334773462	NA	1.88E-09	mr1002_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
vg0334773462	9.26E-06	1.74E-07	mr1648_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
vg0334773462	9.28E-07	NA	mr1670_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