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Detailed information for vg0334698613:

Variant ID: vg0334698613 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34698613
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: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGAAAATAAAAAGGGACTGATTTGGGATACTGAATTCGGTTGAAAATTGATATATAATTGAATCGAAGAAATTAGTGTGACTACTCAATTAGCATCAA[T/C]
CAAGATGTATTATAAAAAGATTTAGCTGAATGGGGAAAGAACTTACGCTGGAACATCTGAGATCAGCAAGCAGTGGAAGTGGAACAACCCCTTTGTTGGC

Reverse complement sequence

GCCAACAAAGGGGTTGTTCCACTTCCACTGCTTGCTGATCTCAGATGTTCCAGCGTAAGTTCTTTCCCCATTCAGCTAAATCTTTTTATAATACATCTTG[A/G]
TTGATGCTAATTGAGTAGTCACACTAATTTCTTCGATTCAATTATATATCAATTTTCAACCGAATTCAGTATCCCAAATCAGTCCCTTTTTATTTTCCCT

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	89.10%	4.10%	5.97%	0.74%	NA
All Indica	2759	81.70%	7.00%	10.08%	1.20%	NA
All Japonica	1512	99.80%	0.00%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.50%	1.01%	0.17%	NA
Indica II	465	92.70%	3.90%	3.44%	0.00%	NA
Indica III	913	63.50%	14.00%	19.93%	2.52%	NA
Indica Intermediate	786	83.70%	5.70%	9.41%	1.15%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334698613	T -> C	LOC_Os03g61070.1	upstream_gene_variant ; 2415.0bp to feature; MODIFIER	silent_mutation	Average:32.5; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0334698613	T -> C	LOC_Os03g61080.2	downstream_gene_variant ; 2225.0bp to feature; MODIFIER	silent_mutation	Average:32.5; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0334698613	T -> C	LOC_Os03g61070-LOC_Os03g61080	intergenic_region ; MODIFIER	silent_mutation	Average:32.5; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0334698613	T -> DEL	N	N	silent_mutation	Average:32.5; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334698613	1.89E-06	NA	mr1496_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