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Detailed information for vg1214554181:

Variant ID: vg1214554181 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14554181
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATCGCCAAAACAAAACAGTGCTGTTGCTGAAACCGAACTTGGGCCTTGGGCTTTGTAATAGATTAGACCCATCTCGGAAGTGTCTCCCTCCACCTCCAC[G/A]
AATTAGCACTTAACCCTAGCTTTATTTTCCTCTATAAATAGCTTTGTACATCCTCAAAAACAATTGGGTTTTGTTTAGTTGAATTTTGCCAAGTGACATT

Reverse complement sequence

AATGTCACTTGGCAAAATTCAACTAAACAAAACCCAATTGTTTTTGAGGATGTACAAAGCTATTTATAGAGGAAAATAAAGCTAGGGTTAAGTGCTAATT[C/T]
GTGGAGGTGGAGGGAGACACTTCCGAGATGGGTCTAATCTATTACAAAGCCCAAGGCCCAAGTTCGGTTTCAGCAACAGCACTGTTTTGTTTTGGCGATT

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	87.30%	12.40%	0.28%	0.00%	NA
All Indica	2759	96.80%	3.00%	0.18%	0.00%	NA
All Japonica	1512	71.30%	28.40%	0.26%	0.00%	NA
Aus	269	80.30%	18.60%	1.12%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	88.40%	11.20%	0.43%	0.00%	NA
Indica III	913	98.20%	1.60%	0.11%	0.00%	NA
Indica Intermediate	786	97.60%	2.20%	0.25%	0.00%	NA
Temperate Japonica	767	90.50%	9.40%	0.13%	0.00%	NA
Tropical Japonica	504	45.80%	53.60%	0.60%	0.00%	NA
Japonica Intermediate	241	63.50%	36.50%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214554181	G -> A	LOC_Os12g25290.1	upstream_gene_variant ; 1465.0bp to feature; MODIFIER	silent_mutation	Average:17.708; most accessible tissue: Zhenshan97 young leaf, score: 40.52	N	N	N	N
vg1214554181	G -> A	LOC_Os12g25280-LOC_Os12g25290	intergenic_region ; MODIFIER	silent_mutation	Average:17.708; most accessible tissue: Zhenshan97 young leaf, score: 40.52	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214554181	NA	1.45E-07	mr1408	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
vg1214554181	NA	5.71E-08	mr1657	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
vg1214554181	NA	1.60E-06	mr1805	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
vg1214554181	2.99E-07	3.00E-07	mr1840	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
vg1214554181	NA	6.32E-06	mr1544_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