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Detailed information for vg0302437930:

Variant ID: vg0302437930 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 2437930
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTCCTAACCTAAGGCTTTCTATCTTTATTTGACTTGATCCTTTGCTGGCACTTGCAGATTTTTTTGAGCACCAGATGGGCCATCTTGTTGAATTTGCA[T/C]
GCCGAGATGTTTCGAACAAATACGTATCCCACTTTTTTTTTTAATAAATGAAGAATATTTCAATGGTTGTATAAATCTTATATATGGTTTCTTTCTAGAA

Reverse complement sequence

TTCTAGAAAGAAACCATATATAAGATTTATACAACCATTGAAATATTCTTCATTTATTAAAAAAAAAAGTGGGATACGTATTTGTTCGAAACATCTCGGC[A/G]
TGCAAATTCAACAAGATGGCCCATCTGGTGCTCAAAAAAATCTGCAAGTGCCAGCAAAGGATCAAGTCAAATAAAGATAGAAAGCCTTAGGTTAGGAAAC

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	92.70%	5.10%	2.18%	0.00%	NA
All Indica	2759	87.60%	8.80%	3.66%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	69.70%	19.20%	11.09%	0.00%	NA
Indica II	465	92.00%	7.50%	0.43%	0.00%	NA
Indica III	913	95.20%	4.30%	0.55%	0.00%	NA
Indica Intermediate	786	89.60%	6.90%	3.56%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	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	97.80%	1.10%	1.11%	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
vg0302437930	T -> C	LOC_Os03g05020.1	intron_variant ; MODIFIER	silent_mutation	Average:33.907; most accessible tissue: Callus, score: 68.03	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0302437930	NA	2.30E-07	mr1274	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
vg0302437930	1.99E-06	1.99E-06	mr1449	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