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Detailed information for vg0229931163:

Variant ID: vg0229931163 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 29931163
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCGGTAGAGTTCTACCAAAGACCGATGATTGCAGTGAACGTACATACGGCGGGGTGCAAGAGGGCAGAAAGATATGCCTCGAGCTGCCAGATCCCGCC[G/A]
TCCTCTTCTTCTAACTTAGAGGTGCTTACATATCATCCCAAACTTTTTTTAATCCACTATAATTTAACATACAAAATTCAAATCTATCAATAGGTTTGGG

Reverse complement sequence

CCCAAACCTATTGATAGATTTGAATTTTGTATGTTAAATTATAGTGGATTAAAAAAAGTTTGGGATGATATGTAAGCACCTCTAAGTTAGAAGAAGAGGA[C/T]
GGCGGGATCTGGCAGCTCGAGGCATATCTTTCTGCCCTCTTGCACCCCGCCGTATGTACGTTCACTGCAATCATCGGTCTTTGGTAGAACTCTACCGCAA

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	98.40%	0.70%	0.87%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	95.20%	2.20%	2.58%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	91.30%	4.20%	4.56%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	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
vg0229931163	G -> A	LOC_Os02g48930.1	upstream_gene_variant ; 4239.0bp to feature; MODIFIER	silent_mutation	Average:53.835; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0229931163	G -> A	LOC_Os02g48940.1	downstream_gene_variant ; 550.0bp to feature; MODIFIER	silent_mutation	Average:53.835; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0229931163	G -> A	LOC_Os02g48950.1	downstream_gene_variant ; 464.0bp to feature; MODIFIER	silent_mutation	Average:53.835; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0229931163	G -> A	LOC_Os02g48964.1	downstream_gene_variant ; 3206.0bp to feature; MODIFIER	silent_mutation	Average:53.835; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0229931163	G -> A	LOC_Os02g48940-LOC_Os02g48950	intergenic_region ; MODIFIER	silent_mutation	Average:53.835; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0229931163	4.28E-06	5.70E-07	mr1008_2	Jap_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