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Detailed information for vg0121350198:

Variant ID: vg0121350198 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21350198
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGTATAGTTGAAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACGTTCCGTCCTTATATATAGATTCATTT[G/A]
TTTCTACCTTATTTCTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGACATTATTAATTATTTGCTACATT

Reverse complement sequence

AATGTAGCAAATAATTAATAATGTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAGAAATAAGGTAGAAA[C/T]
AAATGAATCTATATATAAGGACGGAACGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTTCAACTATACGCA

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	94.90%	5.10%	0.00%	0.00%	NA
All Indica	2759	92.40%	7.60%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	91.40%	8.60%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	80.00%	20.00%	0.00%	0.00%	NA
Indica III	913	96.60%	3.40%	0.00%	0.00%	NA
Indica Intermediate	786	88.90%	11.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0121350198	G -> A	LOC_Os01g38120.1	upstream_gene_variant ; 524.0bp to feature; MODIFIER	silent_mutation	Average:68.338; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350198	G -> A	LOC_Os01g38140.1	upstream_gene_variant ; 4272.0bp to feature; MODIFIER	silent_mutation	Average:68.338; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350198	G -> A	LOC_Os01g38130.1	intron_variant ; MODIFIER	silent_mutation	Average:68.338; most accessible tissue: Callus, score: 80.173	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121350198	NA	2.58E-06	mr1399	Ind_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
vg0121350198	NA	5.05E-06	mr1698	Ind_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