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Detailed information for vg0322407127:

Variant ID: vg0322407127 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22407127
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATCCTTTGATTACCCTTGCATCATACCTTCCACTTGGTATGACTTGTTGTACGGTGGTTGTACTCAGTCTTGCTTTATTTTTCCCAATCCCCCAGAAGCT[A/G]
AGAAAATTTTCCAATCCCCAGAAGCTGAGAATCTGTCAGATTGTGAGTTAGAAGCTGAGAATCTGTCAGATTGTGAGTTCTATGAAGATTAGGCTTGTGC

Reverse complement sequence

GCACAAGCCTAATCTTCATAGAACTCACAATCTGACAGATTCTCAGCTTCTAACTCACAATCTGACAGATTCTCAGCTTCTGGGGATTGGAAAATTTTCT[T/C]
AGCTTCTGGGGGATTGGGAAAAATAAAGCAAGACTGAGTACAACCACCGTACAACAAGTCATACCAAGTGGAAGGTATGATGCAAGGGTAATCAAAGGAT

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	89.50%	7.40%	3.11%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.11%	0.00%	NA
All Japonica	1512	68.70%	22.10%	9.26%	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%	1.10%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	51.40%	34.40%	14.21%	0.00%	NA
Tropical Japonica	504	92.70%	3.40%	3.97%	0.00%	NA
Japonica Intermediate	241	73.40%	22.00%	4.56%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	10.00%	4.44%	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
vg0322407127	A -> G	LOC_Os03g40300.1	downstream_gene_variant ; 3963.0bp to feature; MODIFIER	silent_mutation	Average:32.925; most accessible tissue: Minghui63 flower, score: 52.213	N	N	N	N
vg0322407127	A -> G	LOC_Os03g40300-LOC_Os03g40310	intergenic_region ; MODIFIER	silent_mutation	Average:32.925; most accessible tissue: Minghui63 flower, score: 52.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322407127	6.70E-07	NA	mr1174_2	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