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Detailed information for vg0121584750:

Variant ID: vg0121584750 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21584750
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCACATTCTGCTTGGAATTCTATTCGGGAATTTCTGGGCGTGACAAGTTGGTATCAGAACCGACCTTGACCGTAGGACAAGCCAAATGGAAAAACCTA[G/A]
GAGCCCTCTGAATCCTTTTCATTGCATATGTTCTTTGCAATTTGATTTGTTCCGGGAAAATTGGGATCTGTTCTTGTGGTTCAAGGGAAAAATCTTGGTC

Reverse complement sequence

GACCAAGATTTTTCCCTTGAACCACAAGAACAGATCCCAATTTTCCCGGAACAAATCAAATTGCAAAGAACATATGCAATGAAAAGGATTCAGAGGGCTC[C/T]
TAGGTTTTTCCATTTGGCTTGTCCTACGGTCAAGGTCGGTTCTGATACCAACTTGTCACGCCCAGAAATTCCCGAATAGAATTCCAAGCAGAATGTGCAT

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	36.10%	11.30%	29.64%	22.89%	NA
All Indica	2759	4.20%	18.90%	41.94%	34.90%	NA
All Japonica	1512	96.20%	0.30%	1.12%	2.38%	NA
Aus	269	6.70%	1.10%	67.66%	24.54%	NA
Indica I	595	4.00%	5.90%	22.18%	67.90%	NA
Indica II	465	4.50%	20.20%	23.87%	51.40%	NA
Indica III	913	2.00%	30.20%	59.47%	8.32%	NA
Indica Intermediate	786	6.90%	14.90%	47.20%	31.04%	NA
Temperate Japonica	767	96.50%	0.00%	1.04%	2.48%	NA
Tropical Japonica	504	97.60%	0.80%	1.19%	0.40%	NA
Japonica Intermediate	241	92.50%	0.00%	1.24%	6.22%	NA
VI/Aromatic	96	67.70%	1.00%	27.08%	4.17%	NA
Intermediate	90	57.80%	6.70%	21.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121584750	G -> A	LOC_Os01g38410.1	upstream_gene_variant ; 442.0bp to feature; MODIFIER	silent_mutation	Average:13.644; most accessible tissue: Callus, score: 33.587	N	N	N	N
vg0121584750	G -> A	LOC_Os01g38420.1	upstream_gene_variant ; 2538.0bp to feature; MODIFIER	silent_mutation	Average:13.644; most accessible tissue: Callus, score: 33.587	N	N	N	N
vg0121584750	G -> A	LOC_Os01g38400-LOC_Os01g38410	intergenic_region ; MODIFIER	silent_mutation	Average:13.644; most accessible tissue: Callus, score: 33.587	N	N	N	N
vg0121584750	G -> DEL	N	N	silent_mutation	Average:13.644; most accessible tissue: Callus, score: 33.587	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121584750	NA	3.43E-08	mr1439	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
vg0121584750	NA	6.06E-08	mr1439	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