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Detailed information for vg0316819218:

Variant ID: vg0316819218 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16819218
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAACATCGACAGAAACATCACAGAAAGAGACAAGAGCGATTTTTTTCCCGAAGTTCGGATCTTGCAATCCTACTCTCCGTTGAGGAGCTCCAAAGAGCT[G/A]
GGTCTCAATTAACCCCTTGCCTCACTTGTGCAAAAACCCCAGAAGAAATCCACAGCCTTCAACCCCAAACACCCCTAGGCAAATTTCTAGAATTGAGTGA

Reverse complement sequence

TCACTCAATTCTAGAAATTTGCCTAGGGGTGTTTGGGGTTGAAGGCTGTGGATTTCTTCTGGGGTTTTTGCACAAGTGAGGCAAGGGGTTAATTGAGACC[C/T]
AGCTCTTTGGAGCTCCTCAACGGAGAGTAGGATTGCAAGATCCGAACTTCGGGAAAAAAATCGCTCTTGTCTCTTTCTGTGATGTTTCTGTCGATGTTTC

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	88.50%	10.30%	1.25%	0.00%	NA
All Indica	2759	83.20%	16.60%	0.22%	0.00%	NA
All Japonica	1512	99.30%	0.00%	0.73%	0.00%	NA
Aus	269	77.70%	7.80%	14.50%	0.00%	NA
Indica I	595	57.60%	42.00%	0.34%	0.00%	NA
Indica II	465	95.70%	4.30%	0.00%	0.00%	NA
Indica III	913	88.50%	11.20%	0.33%	0.00%	NA
Indica Intermediate	786	89.10%	10.80%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	0.00%	2.18%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	6.70%	2.22%	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
vg0316819218	G -> A	LOC_Os03g29510.1	upstream_gene_variant ; 1248.0bp to feature; MODIFIER	silent_mutation	Average:36.519; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0316819218	G -> A	LOC_Os03g29520.1	downstream_gene_variant ; 1672.0bp to feature; MODIFIER	silent_mutation	Average:36.519; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0316819218	G -> A	LOC_Os03g29510-LOC_Os03g29520	intergenic_region ; MODIFIER	silent_mutation	Average:36.519; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316819218	3.99E-06	NA	mr1815_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
vg0316819218	1.90E-06	3.99E-06	mr1815_2	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