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Detailed information for vg0432301638:

Variant ID: vg0432301638 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32301638
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGGGACAATTAGTTATTGTTTAGATCTTTAATGTTTTTTATGCTCTCCATTCAGTGAATTATGTAGAGCGGCTGTAGCTCTTTTAAGCAAAGGTTG[A/G]
GAATCTTTCCATTCTCTTAAAAAAATTCCATACCAAATTGAATTGAATTACAGATCTGACTATCATTCAGTAACAAGTGGTAAGTATTAAGTACAAACTA

Reverse complement sequence

TAGTTTGTACTTAATACTTACCACTTGTTACTGAATGATAGTCAGATCTGTAATTCAATTCAATTTGGTATGGAATTTTTTTAAGAGAATGGAAAGATTC[T/C]
CAACCTTTGCTTAAAAGAGCTACAGCCGCTCTACATAATTCACTGAATGGAGAGCATAAAAAACATTAAAGATCTAAACAATAACTAATTGTCCCTAACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	32.10%	0.08%	0.00%	NA
All Indica	2759	92.50%	7.50%	0.07%	0.00%	NA
All Japonica	1512	30.40%	69.50%	0.07%	0.00%	NA
Aus	269	26.40%	73.20%	0.37%	0.00%	NA
Indica I	595	90.40%	9.20%	0.34%	0.00%	NA
Indica II	465	93.50%	6.50%	0.00%	0.00%	NA
Indica III	913	95.80%	4.20%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	10.60%	0.00%	0.00%	NA
Temperate Japonica	767	22.80%	77.20%	0.00%	0.00%	NA
Tropical Japonica	504	45.00%	54.80%	0.20%	0.00%	NA
Japonica Intermediate	241	24.10%	75.90%	0.00%	0.00%	NA
VI/Aromatic	96	69.80%	30.20%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0432301638	A -> G	LOC_Os04g54240.1	3_prime_UTR_variant ; 456.0bp to feature; MODIFIER	silent_mutation	Average:49.347; most accessible tissue: Minghui63 panicle, score: 87.238	N	N	N	N
vg0432301638	A -> G	LOC_Os04g54230.1	upstream_gene_variant ; 3506.0bp to feature; MODIFIER	silent_mutation	Average:49.347; most accessible tissue: Minghui63 panicle, score: 87.238	N	N	N	N
vg0432301638	A -> G	LOC_Os04g54250.1	downstream_gene_variant ; 3179.0bp to feature; MODIFIER	silent_mutation	Average:49.347; most accessible tissue: Minghui63 panicle, score: 87.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432301638	NA	3.57E-08	mr1084_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
vg0432301638	NA	1.13E-07	mr1205_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