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Detailed information for vg0729464249:

Variant ID: vg0729464249 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29464249
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

CATATGTATACATATATGTTGAGTTATTGACCGTATGAAAATACCTGGTAAAGCTAACCACGCTAATTCACAATATTACTAAATATTTCAGAGTATACGA[C/T]
ATTATGTGTTTTAGATTCATACCCAGGTAGGCTATTCTCAATGAGGACTCGAAGACCTTGAGGTGATGTAATACACATTTGAATTATTAAACGTAAACTA

Reverse complement sequence

TAGTTTACGTTTAATAATTCAAATGTGTATTACATCACCTCAAGGTCTTCGAGTCCTCATTGAGAATAGCCTACCTGGGTATGAATCTAAAACACATAAT[G/A]
TCGTATACTCTGAAATATTTAGTAATATTGTGAATTAGCGTGGTTAGCTTTACCAGGTATTTTCATACGGTCAATAACTCAACATATATGTATACATATG

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	62.20%	37.70%	0.11%	0.00%	NA
All Indica	2759	92.10%	7.90%	0.00%	0.00%	NA
All Japonica	1512	13.20%	86.50%	0.33%	0.00%	NA
Aus	269	56.90%	43.10%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	96.10%	3.90%	0.00%	0.00%	NA
Indica III	913	88.10%	11.90%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	10.60%	0.00%	0.00%	NA
Temperate Japonica	767	1.40%	98.20%	0.39%	0.00%	NA
Tropical Japonica	504	21.80%	78.20%	0.00%	0.00%	NA
Japonica Intermediate	241	32.40%	66.80%	0.83%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	46.70%	53.30%	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
vg0729464249	C -> T	LOC_Os07g49200.1	upstream_gene_variant ; 4948.0bp to feature; MODIFIER	silent_mutation	Average:59.78; most accessible tissue: Callus, score: 90.752	N	N	N	N
vg0729464249	C -> T	LOC_Os07g49210.1	upstream_gene_variant ; 924.0bp to feature; MODIFIER	silent_mutation	Average:59.78; most accessible tissue: Callus, score: 90.752	N	N	N	N
vg0729464249	C -> T	LOC_Os07g49200-LOC_Os07g49210	intergenic_region ; MODIFIER	silent_mutation	Average:59.78; most accessible tissue: Callus, score: 90.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729464249	1.73E-06	1.73E-06	mr1173	Jap_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
vg0729464249	NA	2.90E-07	mr1522	Jap_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
vg0729464249	NA	6.73E-07	mr1212_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
vg0729464249	NA	9.25E-08	mr1700_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