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Detailed information for vg0121492519:

Variant ID: vg0121492519 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21492519
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTTACAATCTTTACAGAGTTTTTTCATTTTCTCTTGTTTCTTCCTGTAAATATTACCTGTAATTATTCCTTCAATAAATGAAAATCACACTGCTGGGC[T/A]
AATACCTGGCAGTACTTTCAGTCAAAAAAATAATTATAGAAATTCATTTAAATGCCTCAAAAACTTCTAAAATTCATATATAATTCATTCGAACTCCGAA

Reverse complement sequence

TTCGGAGTTCGAATGAATTATATATGAATTTTAGAAGTTTTTGAGGCATTTAAATGAATTTCTATAATTATTTTTTTGACTGAAAGTACTGCCAGGTATT[A/T]
GCCCAGCAGTGTGATTTTCATTTATTGAAGGAATAATTACAGGTAATATTTACAGGAAGAAACAAGAGAAAATGAAAAAACTCTGTAAAGATTGTAACCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	0.70%	0.55%	53.51%	NA
All Indica	2759	18.10%	1.20%	0.87%	79.81%	NA
All Japonica	1512	97.60%	0.00%	0.07%	2.38%	NA
Aus	269	13.00%	0.00%	0.37%	86.62%	NA
Indica I	595	36.30%	0.20%	0.84%	62.69%	NA
Indica II	465	20.20%	1.10%	0.65%	78.06%	NA
Indica III	913	3.30%	1.50%	0.88%	94.30%	NA
Indica Intermediate	786	20.20%	1.80%	1.02%	76.97%	NA
Temperate Japonica	767	98.40%	0.00%	0.13%	1.43%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	94.60%	0.00%	0.00%	5.39%	NA
VI/Aromatic	96	69.80%	0.00%	0.00%	30.21%	NA
Intermediate	90	67.80%	0.00%	0.00%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121492519	T -> A	LOC_Os01g38310.1	upstream_gene_variant ; 4049.0bp to feature; MODIFIER	silent_mutation	Average:10.886; most accessible tissue: Callus, score: 49.648	N	N	N	N
vg0121492519	T -> A	LOC_Os01g38320.1	upstream_gene_variant ; 1742.0bp to feature; MODIFIER	silent_mutation	Average:10.886; most accessible tissue: Callus, score: 49.648	N	N	N	N
vg0121492519	T -> A	LOC_Os01g38310-LOC_Os01g38320	intergenic_region ; MODIFIER	silent_mutation	Average:10.886; most accessible tissue: Callus, score: 49.648	N	N	N	N
vg0121492519	T -> DEL	N	N	silent_mutation	Average:10.886; most accessible tissue: Callus, score: 49.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121492519	NA	8.74E-14	mr1362	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
vg0121492519	NA	6.83E-06	mr1661	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
vg0121492519	NA	3.17E-09	mr1836	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