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Detailed information for vg0322732625:

Variant ID: vg0322732625 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22732625
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGCGGTGAGGTGATTGGTGCTGGGCGATTGGAGGATTTGACTTCATCAATGCGAACTCCTGAGCATAAATGTCGAGCAATTCAACAAGAGACGAAATC[A/G]
TGTTTTTGAGGAAGGTTGGAACGTTAGAATACATACCGGTGGAGGAGGATTGAATGCATTGAACGGTACGACTGGCAGCAAGTGTGAATAGCTGACAACG

Reverse complement sequence

CGTTGTCAGCTATTCACACTTGCTGCCAGTCGTACCGTTCAATGCATTCAATCCTCCTCCACCGGTATGTATTCTAACGTTCCAACCTTCCTCAAAAACA[T/C]
GATTTCGTCTCTTGTTGAATTGCTCGACATTTATGCTCAGGAGTTCGCATTGATGAAGTCAAATCCTCCAATCGCCCAGCACCAATCACCTCACCGCCAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.00%	23.90%	5.42%	15.74%	NA
All Indica	2759	25.70%	39.80%	8.99%	25.52%	NA
All Japonica	1512	99.40%	0.00%	0.20%	0.40%	NA
Aus	269	88.50%	7.10%	0.37%	4.09%	NA
Indica I	595	31.40%	34.30%	13.28%	21.01%	NA
Indica II	465	18.30%	27.70%	13.12%	40.86%	NA
Indica III	913	20.50%	54.20%	5.48%	19.82%	NA
Indica Intermediate	786	31.90%	34.20%	7.38%	26.46%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	0.00%	0.20%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	61.10%	13.30%	4.44%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322732625	A -> DEL	N	N	silent_mutation	Average:10.826; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0322732625	A -> G	LOC_Os03g40900.1	upstream_gene_variant ; 4071.0bp to feature; MODIFIER	silent_mutation	Average:10.826; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0322732625	A -> G	LOC_Os03g40870.1	downstream_gene_variant ; 3181.0bp to feature; MODIFIER	silent_mutation	Average:10.826; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0322732625	A -> G	LOC_Os03g40880.1	intron_variant ; MODIFIER	silent_mutation	Average:10.826; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322732625	9.74E-07	9.74E-07	mr1321	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
vg0322732625	NA	2.58E-07	mr1881	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