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Detailed information for vg0205684729:

Variant ID: vg0205684729 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5684729
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAGTTGGGAAGCATCCAACCACTCGATCAGCCTCATTGCTTATGCTTATCATCCAGAATTTGAATTTCCAACCTTAATTTAAGTTGATTTAAAAAAAAA[T/A]
TTACCGTAGTTTATTTTTCAGTTTTTTGCTTTTAGATCGTTAAGAACACGTATATAAAAGTTGTATTCACAAATTATTTTTCATTTGTAAATATGTCGTT

Reverse complement sequence

AACGACATATTTACAAATGAAAAATAATTTGTGAATACAACTTTTATATACGTGTTCTTAACGATCTAAAAGCAAAAAACTGAAAAATAAACTACGGTAA[A/T]
TTTTTTTTTAAATCAACTTAAATTAAGGTTGGAAATTCAAATTCTGGATGATAAGCATAAGCAATGAGGCTGATCGAGTGGTTGGATGCTTCCCAACTTT

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	95.80%	3.20%	0.97%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	87.60%	9.50%	2.98%	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	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	93.60%	2.10%	4.30%	0.00%	NA
Tropical Japonica	504	78.20%	20.40%	1.39%	0.00%	NA
Japonica Intermediate	241	88.00%	10.00%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0205684729	T -> A	LOC_Os02g10760.1	upstream_gene_variant ; 3969.0bp to feature; MODIFIER	silent_mutation	Average:57.967; most accessible tissue: Callus, score: 87.425	N	N	N	N
vg0205684729	T -> A	LOC_Os02g10750-LOC_Os02g10760	intergenic_region ; MODIFIER	silent_mutation	Average:57.967; most accessible tissue: Callus, score: 87.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205684729	3.64E-06	1.18E-07	mr1905_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