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Detailed information for vg0335613340:

Variant ID: vg0335613340 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35613340
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TATTATCTAGTAAGTCAGAAGAATCCTCAAGACCTAGGGTTAAATATAAAATTCAAATTCAAAAGAAATTCAAATGAAATCCAAAAATAGGGCAAAATAA[C/T,A]
ATAAAATGAGAATAGCAAAAAAAAAGCTTTAGAAGGTAGAGAATGATTTTAGAAGAATTTTGGTCTAAGTTTCATTAGAATTGGGTTTATATTTAAAAGA

Reverse complement sequence

TCTTTTAAATATAAACCCAATTCTAATGAAACTTAGACCAAAATTCTTCTAAAATCATTCTCTACCTTCTAAAGCTTTTTTTTTGCTATTCTCATTTTAT[G/A,T]
TTATTTTGCCCTATTTTTGGATTTCATTTGAATTTCTTTTGAATTTGAATTTTATATTTAACCCTAGGTCTTGAGGATTCTTCTGACTTACTAGATAATA

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	86.50%	13.00%	0.25%	0.30%	NA
All Indica	2759	83.30%	15.80%	0.43%	0.51%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	43.90%	56.10%	0.00%	0.00%	NA
Indica I	595	93.80%	5.40%	0.67%	0.17%	NA
Indica II	465	91.20%	8.60%	0.22%	0.00%	NA
Indica III	913	69.40%	29.60%	0.00%	0.99%	NA
Indica Intermediate	786	86.80%	11.80%	0.89%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0335613340	C -> T	LOC_Os03g62974.1	downstream_gene_variant ; 2048.0bp to feature; MODIFIER	silent_mutation	Average:27.774; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0335613340	C -> T	LOC_Os03g62950-LOC_Os03g62974	intergenic_region ; MODIFIER	silent_mutation	Average:27.774; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0335613340	C -> A	LOC_Os03g62974.1	downstream_gene_variant ; 2048.0bp to feature; MODIFIER	N	Average:27.774; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0335613340	C -> A	LOC_Os03g62950-LOC_Os03g62974	intergenic_region ; MODIFIER	N	Average:27.774; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0335613340	C -> DEL	N	N	silent_mutation	Average:27.774; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335613340	4.00E-06	5.84E-06	mr1120	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