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Detailed information for vg1214088177:

Variant ID: vg1214088177 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14088177
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTTCCAAACACCAAAACATTTTTTTGATGGGTTTGCCAATGTGTTCATAAGGGGGAGATTGTAAAATCAAAGGTGTTTTTTATTATTATTTTGTGAT[G/A]
AACAATTGGCATCGGAGATTATTGGTTTTGTTATTTGGAATTTATTTACGAAGTGGTTTTGGAGATGATTGGATTTACAGCTGAATCTACAGGATACTGC

Reverse complement sequence

GCAGTATCCTGTAGATTCAGCTGTAAATCCAATCATCTCCAAAACCACTTCGTAAATAAATTCCAAATAACAAAACCAATAATCTCCGATGCCAATTGTT[C/T]
ATCACAAAATAATAATAAAAAACACCTTTGATTTTACAATCTCCCCCTTATGAACACATTGGCAAACCCATCAAAAAAATGTTTTGGTGTTTGGAAAAAT

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	91.60%	7.90%	0.25%	0.25%	NA
All Indica	2759	86.20%	13.00%	0.43%	0.40%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	79.50%	18.70%	1.34%	0.50%	NA
Indica II	465	96.30%	3.20%	0.43%	0.00%	NA
Indica III	913	87.00%	12.40%	0.00%	0.66%	NA
Indica Intermediate	786	84.40%	15.10%	0.25%	0.25%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214088177	G -> DEL	N	N	silent_mutation	Average:34.499; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1214088177	G -> A	LOC_Os12g24610.1	downstream_gene_variant ; 3278.0bp to feature; MODIFIER	silent_mutation	Average:34.499; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1214088177	G -> A	LOC_Os12g24620.1	downstream_gene_variant ; 4127.0bp to feature; MODIFIER	silent_mutation	Average:34.499; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg1214088177	G -> A	LOC_Os12g24610-LOC_Os12g24620	intergenic_region ; MODIFIER	silent_mutation	Average:34.499; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214088177	NA	9.24E-06	mr1177	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
vg1214088177	NA	2.06E-06	mr1177	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
vg1214088177	NA	6.83E-06	mr1327	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
vg1214088177	NA	1.92E-07	mr1336	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
vg1214088177	NA	2.62E-06	mr1579	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
vg1214088177	NA	2.48E-07	mr1701	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