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Detailed information for vg0317492428:

Variant ID: vg0317492428 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17492428
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGCTATTTAATTAGGCAACATTAGGTGGTTTTACAACTCTAGACTTTGGGAATATTCATATTGCTTGGACATTATGGAATGGTTGGATTATTGTGGAA[C/T]
TGGATTCACACCTCCCCCTCTATTCAAAACCCTCAAAATGGTTTTAGGCTGGGCTCGGGGTGCATGGTTTTGATAGTAGCACCTCGGCCACATAAGGACC

Reverse complement sequence

GGTCCTTATGTGGCCGAGGTGCTACTATCAAAACCATGCACCCCGAGCCCAGCCTAAAACCATTTTGAGGGTTTTGAATAGAGGGGGAGGTGTGAATCCA[G/A]
TTCCACAATAATCCAACCATTCCATAATGTCCAAGCAATATGAATATTCCCAAAGTCTAGAGTTGTAAAACCACCTAATGTTGCCTAATTAAATAGCGAA

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	67.10%	32.80%	0.11%	0.00%	NA
All Indica	2759	98.10%	1.90%	0.04%	0.00%	NA
All Japonica	1512	5.50%	94.50%	0.00%	0.00%	NA
Aus	269	90.00%	9.70%	0.37%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	3.10%	0.00%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	15.10%	84.90%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	58.90%	37.80%	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
vg0317492428	C -> T	LOC_Os03g30710.1	upstream_gene_variant ; 3414.0bp to feature; MODIFIER	silent_mutation	Average:19.945; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0317492428	C -> T	LOC_Os03g30700.1	downstream_gene_variant ; 1898.0bp to feature; MODIFIER	silent_mutation	Average:19.945; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0317492428	C -> T	LOC_Os03g30700-LOC_Os03g30710	intergenic_region ; MODIFIER	silent_mutation	Average:19.945; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317492428	NA	2.81E-19	mr1021	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
vg0317492428	NA	5.11E-10	mr1175	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
vg0317492428	8.78E-07	3.02E-09	mr1718	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
vg0317492428	NA	1.43E-09	mr1750	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
vg0317492428	NA	9.80E-40	mr1243_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
vg0317492428	NA	2.22E-11	mr1377_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
vg0317492428	NA	4.69E-14	mr1750_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