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Detailed information for vg0224638374:

Variant ID: vg0224638374 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24638374
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTACGTCCCAAAATAATCACTTCATAAATACTTTTAGAAAAATGAGGTGTGAAATTGAATGAGTATAGGTTGTGACTAGATTAAGATAAAGAAATACGC[A/G]
AAAAAATTAAACAAAAAATAGTTTAGATGAAATAGAAGGGGAAATAAAATGCGAGATGTTGTGATTAGTTTAGATGAGGAGGGAATGTCTAATTAGCGCA

Reverse complement sequence

TGCGCTAATTAGACATTCCCTCCTCATCTAAACTAATCACAACATCTCGCATTTTATTTCCCCTTCTATTTCATCTAAACTATTTTTTGTTTAATTTTTT[T/C]
GCGTATTTCTTTATCTTAATCTAGTCACAACCTATACTCATTCAATTTCACACCTCATTTTTCTAAAAGTATTTATGAAGTGATTATTTTGGGACGTACA

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	84.90%	15.00%	0.08%	0.00%	NA
All Indica	2759	94.50%	5.50%	0.04%	0.00%	NA
All Japonica	1512	65.30%	34.50%	0.13%	0.00%	NA
Aus	269	95.20%	4.50%	0.37%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	92.90%	7.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.30%	8.50%	0.13%	0.00%	NA
Temperate Japonica	767	57.60%	42.20%	0.13%	0.00%	NA
Tropical Japonica	504	73.00%	27.00%	0.00%	0.00%	NA
Japonica Intermediate	241	73.90%	25.70%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg0224638374	A -> G	LOC_Os02g40630.1	upstream_gene_variant ; 2375.0bp to feature; MODIFIER	silent_mutation	Average:33.584; most accessible tissue: Callus, score: 55.413	N	N	N	N
vg0224638374	A -> G	LOC_Os02g40640.1	downstream_gene_variant ; 2909.0bp to feature; MODIFIER	silent_mutation	Average:33.584; most accessible tissue: Callus, score: 55.413	N	N	N	N
vg0224638374	A -> G	LOC_Os02g40630-LOC_Os02g40640	intergenic_region ; MODIFIER	silent_mutation	Average:33.584; most accessible tissue: Callus, score: 55.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224638374	1.70E-08	NA	mr1841	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