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Detailed information for vg0401708881:

Variant ID: vg0401708881 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1708881
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTACACTATTCTAACTAATATTGTATCTATAACTTCTTTGGAGCGTTTATTAGCGCATAAAAAATCGATGGGCTAGCAACATTGATTTAGCATTTCA[A/G]
CCAAATACAGTTAGGAAGAACTATCATAGTATGTTCTCACCACTGAGCCTGTAAAACAAGTAACTGAAAAACGGAAATTAAGGAAGCGCATAAGTGTCAG

Reverse complement sequence

CTGACACTTATGCGCTTCCTTAATTTCCGTTTTTCAGTTACTTGTTTTACAGGCTCAGTGGTGAGAACATACTATGATAGTTCTTCCTAACTGTATTTGG[T/C]
TGAAATGCTAAATCAATGTTGCTAGCCCATCGATTTTTTATGCGCTAATAAACGCTCCAAAGAAGTTATAGATACAATATTAGTTAGAATAGTGTAATAA

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	48.20%	30.30%	0.97%	20.59%	NA
All Indica	2759	67.60%	11.60%	1.12%	19.61%	NA
All Japonica	1512	13.90%	63.40%	0.73%	22.02%	NA
Aus	269	42.40%	40.50%	0.74%	16.36%	NA
Indica I	595	71.30%	23.40%	1.34%	4.03%	NA
Indica II	465	51.60%	9.90%	1.51%	36.99%	NA
Indica III	913	79.20%	2.00%	0.55%	18.29%	NA
Indica Intermediate	786	60.90%	15.00%	1.40%	22.65%	NA
Temperate Japonica	767	12.10%	74.70%	0.52%	12.65%	NA
Tropical Japonica	504	19.60%	48.60%	1.19%	30.56%	NA
Japonica Intermediate	241	7.50%	58.10%	0.41%	34.02%	NA
VI/Aromatic	96	51.00%	12.50%	1.04%	35.42%	NA
Intermediate	90	41.10%	34.40%	1.11%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401708881	A -> DEL	N	N	silent_mutation	Average:26.248; most accessible tissue: Callus, score: 48.071	N	N	N	N
vg0401708881	A -> G	LOC_Os04g03796.4	downstream_gene_variant ; 2217.0bp to feature; MODIFIER	silent_mutation	Average:26.248; most accessible tissue: Callus, score: 48.071	N	N	N	N
vg0401708881	A -> G	LOC_Os04g03796.1	intron_variant ; MODIFIER	silent_mutation	Average:26.248; most accessible tissue: Callus, score: 48.071	N	N	N	N
vg0401708881	A -> G	LOC_Os04g03796.2	intron_variant ; MODIFIER	silent_mutation	Average:26.248; most accessible tissue: Callus, score: 48.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401708881	NA	9.55E-06	mr1855_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