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Detailed information for vg0103188464:

Variant ID: vg0103188464 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3188464
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.35, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAACTTTGGATCTAAACACGGCCTAAGGAACTAAACACAGCCATTGTGCGGTTCCTCTTTTCTGGATTGG[A/G]
ATTTGGCCTTGGATTTGCCATTGCAATTGCAATAGCATGGGGGAATTCCCATCAGAAAACGGTCTCCAGTAGGTCGGAGAGCTCTCTGAATTCTGTATTA

Reverse complement sequence

TAATACAGAATTCAGAGAGCTCTCCGACCTACTGGAGACCGTTTTCTGATGGGAATTCCCCCATGCTATTGCAATTGCAATGGCAAATCCAAGGCCAAAT[T/C]
CCAATCCAGAAAAGAGGAACCGCACAATGGCTGTGTTTAGTTCCTTAGGCCGTGTTTAGATCCAAAGTTTTTCTTCAAACTTTCAACTTTTTCATCACAT

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	27.30%	13.90%	0.34%	58.51%	NA
All Indica	2759	6.10%	5.40%	0.40%	88.11%	NA
All Japonica	1512	71.10%	13.50%	0.26%	15.15%	NA
Aus	269	6.30%	85.90%	0.00%	7.81%	NA
Indica I	595	1.80%	3.90%	0.17%	94.12%	NA
Indica II	465	3.20%	7.50%	0.65%	88.60%	NA
Indica III	913	10.80%	5.40%	0.11%	83.68%	NA
Indica Intermediate	786	5.50%	5.30%	0.76%	88.42%	NA
Temperate Japonica	767	63.60%	19.60%	0.52%	16.30%	NA
Tropical Japonica	504	81.50%	3.20%	0.00%	15.28%	NA
Japonica Intermediate	241	73.00%	15.80%	0.00%	11.20%	NA
VI/Aromatic	96	1.00%	52.10%	0.00%	46.88%	NA
Intermediate	90	31.10%	24.40%	1.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103188464	A -> G	LOC_Os01g06730.1	downstream_gene_variant ; 3118.0bp to feature; MODIFIER	silent_mutation	Average:10.507; most accessible tissue: Callus, score: 54.982	N	N	N	N
vg0103188464	A -> G	LOC_Os01g06740.1	downstream_gene_variant ; 293.0bp to feature; MODIFIER	silent_mutation	Average:10.507; most accessible tissue: Callus, score: 54.982	N	N	N	N
vg0103188464	A -> G	LOC_Os01g06730-LOC_Os01g06740	intergenic_region ; MODIFIER	silent_mutation	Average:10.507; most accessible tissue: Callus, score: 54.982	N	N	N	N
vg0103188464	A -> DEL	N	N	silent_mutation	Average:10.507; most accessible tissue: Callus, score: 54.982	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103188464	1.63E-06	1.63E-06	mr1317	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
vg0103188464	5.46E-06	5.45E-06	mr1520	Jap_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
vg0103188464	NA	4.85E-06	mr1897	Jap_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