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Detailed information for vg0417267842:

Variant ID: vg0417267842 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17267842
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, T: 0.16, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

AACCTGAATTTAGGAAGAAATCTTTAAATGGGGGGAGAAACAGGTTAGCTGGAGGTGATACAGTATACCAATGCGGCGGGTCGCGAGGCTTGGTTGCTAC[G/T]
AAACTGTACCTGGTGCTTGTTAATTTGTAGCAATTCATAGGGCTTGTTCCTATATAAAATCGTTGCATATACTAATTTATTTGTAATGTAGCAACATAAA

Reverse complement sequence

TTTATGTTGCTACATTACAAATAAATTAGTATATGCAACGATTTTATATAGGAACAAGCCCTATGAATTGCTACAAATTAACAAGCACCAGGTACAGTTT[C/A]
GTAGCAACCAAGCCTCGCGACCCGCCGCATTGGTATACTGTATCACCTCCAGCTAACCTGTTTCTCCCCCCATTTAAAGATTTCTTCCTAAATTCAGGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.80%	12.10%	0.11%	0.00%	NA
All Indica	2759	94.80%	5.20%	0.00%	0.00%	NA
All Japonica	1512	75.00%	24.70%	0.33%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	79.70%	20.30%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	57.90%	41.50%	0.65%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	78.80%	21.20%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0417267842	G -> T	LOC_Os04g29090.1	upstream_gene_variant ; 4710.0bp to feature; MODIFIER	silent_mutation	Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0417267842	G -> T	LOC_Os04g29100.1	upstream_gene_variant ; 1198.0bp to feature; MODIFIER	silent_mutation	Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg0417267842	G -> T	LOC_Os04g29090-LOC_Os04g29100	intergenic_region ; MODIFIER	silent_mutation	Average:48.261; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417267842	5.77E-07	NA	mr1137_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
vg0417267842	6.66E-08	NA	mr1617_2	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