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Detailed information for vg0725152187:

Variant ID: vg0725152187 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25152187
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

TGTGCTATAATAAATTAAATTGCTGCATATGTGATGTTGTAAATTGTTGCTTTGTGATGGATCTGTGATATGTGATGCATCTGTGATGTTGGGCAGTTGG[A/G]
GAATATGTGATATGGGATGGTGATTGGCACCTGTGATGTTTCTGTTTTTCAGAGGGCATGGCTAGCAATTCCTGAGGCTAGCCAATATTTAGCATTTATT

Reverse complement sequence

AATAAATGCTAAATATTGGCTAGCCTCAGGAATTGCTAGCCATGCCCTCTGAAAAACAGAAACATCACAGGTGCCAATCACCATCCCATATCACATATTC[T/C]
CCAACTGCCCAACATCACAGATGCATCACATATCACAGATCCATCACAAAGCAACAATTTACAACATCACATATGCAGCAATTTAATTTATTATAGCACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.20%	12.10%	17.73%	43.04%	NA
All Indica	2759	5.40%	8.80%	27.91%	57.81%	NA
All Japonica	1512	66.50%	4.00%	2.98%	26.52%	NA
Aus	269	1.50%	92.90%	4.83%	0.74%	NA
Indica I	595	3.50%	17.80%	8.91%	69.75%	NA
Indica II	465	12.30%	1.90%	24.73%	61.08%	NA
Indica III	913	1.90%	6.40%	44.36%	47.43%	NA
Indica Intermediate	786	7.00%	9.00%	25.06%	58.91%	NA
Temperate Japonica	767	45.80%	0.70%	5.22%	48.37%	NA
Tropical Japonica	504	88.90%	10.30%	0.20%	0.60%	NA
Japonica Intermediate	241	85.90%	1.20%	1.66%	11.20%	NA
VI/Aromatic	96	83.30%	2.10%	4.17%	10.42%	NA
Intermediate	90	48.90%	15.60%	6.67%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0725152187	A -> DEL	N	N	silent_mutation	Average:12.065; most accessible tissue: Callus, score: 56.006	N	N	N	N
vg0725152187	A -> G	LOC_Os07g42030.1	upstream_gene_variant ; 4730.0bp to feature; MODIFIER	silent_mutation	Average:12.065; most accessible tissue: Callus, score: 56.006	N	N	N	N
vg0725152187	A -> G	LOC_Os07g42020.1	downstream_gene_variant ; 591.0bp to feature; MODIFIER	silent_mutation	Average:12.065; most accessible tissue: Callus, score: 56.006	N	N	N	N
vg0725152187	A -> G	LOC_Os07g42020-LOC_Os07g42030	intergenic_region ; MODIFIER	silent_mutation	Average:12.065; most accessible tissue: Callus, score: 56.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0725152187	4.78E-06	4.78E-06	mr1447	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
vg0725152187	NA	6.77E-06	mr1970	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
vg0725152187	NA	2.44E-06	mr1360_2	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
vg0725152187	NA	6.38E-08	mr1707_2	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