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Detailed information for vg0410434829:

Variant ID: vg0410434829 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10434829
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.35, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAGAACTTCACTCTCTGTCTTGATTTGAAAAAATCCTATCGAGTGAGTTTTTCTAAGTATCGGAGTATCCGATGTCGGATCAGATAGTCCGATGATA[C/T]
AGAGACTCCGAAATTTCATAGAACTTGAGTCTCTGTTTGAGGACGAAATTTTTGCTTCTAAAATATCAGATATTCCGATTTAACATCAGATAGTCTGATG

Reverse complement sequence

CATCAGACTATCTGATGTTAAATCGGAATATCTGATATTTTAGAAGCAAAAATTTCGTCCTCAAACAGAGACTCAAGTTCTATGAAATTTCGGAGTCTCT[G/A]
TATCATCGGACTATCTGATCCGACATCGGATACTCCGATACTTAGAAAAACTCACTCGATAGGATTTTTTCAAATCAAGACAGAGAGTGAAGTTCTGTGA

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	64.80%	35.10%	0.02%	0.00%	NA
All Indica	2759	98.60%	1.40%	0.04%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.20%	1.70%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	50.00%	50.00%	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
vg0410434829	C -> T	LOC_Os04g18770.1	upstream_gene_variant ; 781.0bp to feature; MODIFIER	silent_mutation	Average:23.858; most accessible tissue: Callus, score: 34.41	N	N	N	N
vg0410434829	C -> T	LOC_Os04g18760-LOC_Os04g18770	intergenic_region ; MODIFIER	silent_mutation	Average:23.858; most accessible tissue: Callus, score: 34.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410434829	1.21E-06	NA	mr1645	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
vg0410434829	5.91E-06	8.87E-06	mr1645	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