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Detailed information for vg0717342657:

Variant ID: vg0717342657 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 17342657
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCAGGAGGCTTTGGATCGTTTTCACCCTCACCACTTGGTCTTATCCAACCTTGGCAGGTATAAAGCTAGTTATTTTGGATAGTGGTTCTATGATTGCT[C/T]
GGTGTGATGGGTCGGATTCCAGGAGACTTTGGATCGTTTTCACCCTCACCACTTGGTCACATCTGACCTTGTCAGGTATAAAGCTAGTTATCTTCTAGCT

Reverse complement sequence

AGCTAGAAGATAACTAGCTTTATACCTGACAAGGTCAGATGTGACCAAGTGGTGAGGGTGAAAACGATCCAAAGTCTCCTGGAATCCGACCCATCACACC[G/A]
AGCAATCATAGAACCACTATCCAAAATAACTAGCTTTATACCTGCCAAGGTTGGATAAGACCAAGTGGTGAGGGTGAAAACGATCCAAAGCCTCCTGGAC

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	66.20%	32.40%	0.08%	1.33%	NA
All Indica	2759	45.00%	53.60%	0.04%	1.30%	NA
All Japonica	1512	97.40%	0.60%	0.20%	1.79%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	42.50%	53.90%	0.00%	3.53%	NA
Indica II	465	24.50%	75.50%	0.00%	0.00%	NA
Indica III	913	52.60%	46.90%	0.11%	0.44%	NA
Indica Intermediate	786	50.30%	48.30%	0.00%	1.40%	NA
Temperate Japonica	767	99.00%	0.80%	0.13%	0.13%	NA
Tropical Japonica	504	96.40%	0.20%	0.40%	2.98%	NA
Japonica Intermediate	241	94.60%	0.80%	0.00%	4.56%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0717342657	C -> DEL	N	N	silent_mutation	Average:53.558; most accessible tissue: Zhenshan97 young leaf, score: 82.763	N	N	N	N
vg0717342657	C -> T	LOC_Os07g29540.1	intron_variant ; MODIFIER	silent_mutation	Average:53.558; most accessible tissue: Zhenshan97 young leaf, score: 82.763	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0717342657	NA	1.05E-06	mr1107	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
vg0717342657	NA	5.01E-07	mr1155	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
vg0717342657	1.85E-06	1.33E-06	mr1241	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
vg0717342657	NA	5.24E-08	mr1155_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
vg0717342657	NA	1.28E-10	mr1174_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
vg0717342657	NA	4.92E-06	mr1246_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
vg0717342657	NA	3.99E-07	mr1548_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