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Detailed information for vg0124773317:

Variant ID: vg0124773317 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24773317
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGACATTGTGTTTTACTGTTTACATAGTTTAGATATAATATGTTTTTTTACTAAAAATACAATATTTGCTAATCTTAAAAAATAAAGCAGGTGCAGATC[C/T]
AGAAAATGGAGTCATTGAGGTCACTACTCAAATATAATGGTGTCAATACATATATAAGAGAGTAATTCTTGTTTCTATAGTGTATTAGCAAAGCTGACAT

Reverse complement sequence

ATGTCAGCTTTGCTAATACACTATAGAAACAAGAATTACTCTCTTATATATGTATTGACACCATTATATTTGAGTAGTGACCTCAATGACTCCATTTTCT[G/A]
GATCTGCACCTGCTTTATTTTTTAAGATTAGCAAATATTGTATTTTTAGTAAAAAAACATATTATATCTAAACTATGTAAACAGTAAAACACAATGTCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.00%	3.90%	0.06%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	89.90%	9.90%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	82.50%	17.20%	0.26%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.40%	0.41%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0124773317	C -> T	LOC_Os01g43340.1	upstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:70.436; most accessible tissue: Callus, score: 86.214	N	N	N	N
vg0124773317	C -> T	LOC_Os01g43330-LOC_Os01g43340	intergenic_region ; MODIFIER	silent_mutation	Average:70.436; most accessible tissue: Callus, score: 86.214	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124773317	4.79E-07	NA	mr1062	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
vg0124773317	NA	4.18E-08	mr1062	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