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Detailed information for vg0329080105:

Variant ID: vg0329080105 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 29080105
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCAAATATGCTATGGATTAAAGATGGACTAACCAGCTCAGAGCTACAGGTGCTCAGTAGTGCGAGTTTTAGTACTGAAGTGCTGTGGTTACAGCCCTT[C/T]
AACTGCAAAGTGATCCAGTTATTCTTCCATTGTCCTTCAACAGAGGAGCTTGCATGGTGCAATATGTTCCAGGACCCATGACCACAAGGAGGCCAGAGAG

Reverse complement sequence

CTCTCTGGCCTCCTTGTGGTCATGGGTCCTGGAACATATTGCACCATGCAAGCTCCTCTGTTGAAGGACAATGGAAGAATAACTGGATCACTTTGCAGTT[G/A]
AAGGGCTGTAACCACAGCACTTCAGTACTAAAACTCGCACTACTGAGCACCTGTAGCTCTGAGCTGGTTAGTCCATCTTTAATCCATAGCATATTTGGAT

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	98.90%	1.00%	0.17%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.07%	0.00%	NA
All Japonica	1512	97.40%	2.20%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	94.90%	4.30%	0.78%	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	98.90%	1.10%	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
vg0329080105	C -> T	LOC_Os03g50900.1	upstream_gene_variant ; 800.0bp to feature; MODIFIER	silent_mutation	Average:64.612; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg0329080105	C -> T	LOC_Os03g50885.1	downstream_gene_variant ; 4235.0bp to feature; MODIFIER	silent_mutation	Average:64.612; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg0329080105	C -> T	LOC_Os03g50900-LOC_Os03g50920	intergenic_region ; MODIFIER	silent_mutation	Average:64.612; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0329080105	NA	1.53E-06	mr1712	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
vg0329080105	3.71E-06	3.71E-06	mr1717	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