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Detailed information for vg0229815178:

Variant ID: vg0229815178 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 29815178
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAATCATATAGGACTTTTTTTTATGTGCCTATTTGATTCACTGATTGAAACTTTTCAGATACTATAGAATTTATATGGAATGGTTCATTTTATATATT[T/G]
TTTGAAGAAAACTTAGTAAGAGCTCTAATCTTGTGGGAAATTTTTAGATTCATGTGTTTTTCTACGGTTCAATTAAACATTCATTCATGTGTTTTTTTAA

Reverse complement sequence

TTAAAAAAACACATGAATGAATGTTTAATTGAACCGTAGAAAAACACATGAATCTAAAAATTTCCCACAAGATTAGAGCTCTTACTAAGTTTTCTTCAAA[A/C]
AATATATAAAATGAACCATTCCATATAAATTCTATAGTATCTGAAAAGTTTCAATCAGTGAATCAAATAGGCACATAAAAAAAAGTCCTATATGATTTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.90%	1.50%	0.57%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.70%	4.60%	1.72%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	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	87.90%	8.70%	3.39%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0229815178	T -> G	LOC_Os02g48710.1	downstream_gene_variant ; 1423.0bp to feature; MODIFIER	silent_mutation	Average:38.502; most accessible tissue: Callus, score: 81.462	N	N	N	N
vg0229815178	T -> G	LOC_Os02g48710-LOC_Os02g48720	intergenic_region ; MODIFIER	silent_mutation	Average:38.502; most accessible tissue: Callus, score: 81.462	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0229815178	3.36E-07	3.36E-07	mr1004_2	Jap_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