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Detailed information for vg1117548109:

Variant ID: vg1117548109 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17548109
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.88, G: 0.12, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGGGATTATATACTACGTATTAAATTTTAGTCCCGGTTGGTGAGCTATGGTGTTTTTAACCGGGACTGAAGATCATTTTTAGTCCCGGTTTTTATCGC[G/A]
ATCGGGACTATTGTGGATTTTGGCCGACCGACCATAGATGGTTTCTCCACCAGTGATGGCTACGGAGCGGAAAGGAAGATTGAAGTGCGCCAGATGGGAA

Reverse complement sequence

TTCCCATCTGGCGCACTTCAATCTTCCTTTCCGCTCCGTAGCCATCACTGGTGGAGAAACCATCTATGGTCGGTCGGCCAAAATCCACAATAGTCCCGAT[C/T]
GCGATAAAAACCGGGACTAAAAATGATCTTCAGTCCCGGTTAAAAACACCATAGCTCACCAACCGGGACTAAAATTTAATACGTAGTATATAATCCCTAT

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	31.10%	24.30%	0.44%	44.12%	NA
All Indica	2759	5.10%	30.80%	0.65%	63.47%	NA
All Japonica	1512	82.10%	1.10%	0.07%	16.80%	NA
Aus	269	4.80%	85.10%	0.00%	10.04%	NA
Indica I	595	11.80%	17.00%	0.34%	70.92%	NA
Indica II	465	3.40%	32.00%	0.65%	63.87%	NA
Indica III	913	1.60%	37.10%	0.33%	60.90%	NA
Indica Intermediate	786	5.00%	33.20%	1.27%	60.56%	NA
Temperate Japonica	767	97.50%	0.10%	0.00%	2.35%	NA
Tropical Japonica	504	57.50%	1.40%	0.20%	40.87%	NA
Japonica Intermediate	241	84.20%	3.30%	0.00%	12.45%	NA
VI/Aromatic	96	46.90%	28.10%	1.04%	23.96%	NA
Intermediate	90	36.70%	28.90%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117548109	G -> A	LOC_Os11g30170.1	upstream_gene_variant ; 4298.0bp to feature; MODIFIER	silent_mutation	Average:7.889; most accessible tissue: Callus, score: 23.513	N	N	N	N
vg1117548109	G -> A	LOC_Os11g30190.1	upstream_gene_variant ; 56.0bp to feature; MODIFIER	silent_mutation	Average:7.889; most accessible tissue: Callus, score: 23.513	N	N	N	N
vg1117548109	G -> A	LOC_Os11g30180.1	downstream_gene_variant ; 2375.0bp to feature; MODIFIER	silent_mutation	Average:7.889; most accessible tissue: Callus, score: 23.513	N	N	N	N
vg1117548109	G -> A	LOC_Os11g30180-LOC_Os11g30190	intergenic_region ; MODIFIER	silent_mutation	Average:7.889; most accessible tissue: Callus, score: 23.513	N	N	N	N
vg1117548109	G -> DEL	N	N	silent_mutation	Average:7.889; most accessible tissue: Callus, score: 23.513	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117548109	NA	6.94E-07	mr1170	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
vg1117548109	3.98E-06	3.97E-06	mr1329	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
vg1117548109	NA	2.77E-06	mr1708	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
vg1117548109	NA	2.24E-06	mr1729	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
vg1117548109	NA	2.05E-08	mr1896	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
vg1117548109	8.67E-06	8.67E-06	mr1947	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