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Detailed information for vg0401777097:

Variant ID: vg0401777097 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1777097
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, T: 0.27, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGATTCATTAATATTTACATTTCTCGATGCCCATGCAACCAATCTTGTGTGGAAGAATGAAGAGTCATGCATTAAATCCAAGAAAGTCATTAAGATGA[A/T]
AAGTTGTTGGATTGAAATATGACTATCAAAAATAAAATTTTCAGATTTGGAAATATGACTATCAAAAGTAGATGGAGGGAGTATTTGTACCCAATTCTAG

Reverse complement sequence

CTAGAATTGGGTACAAATACTCCCTCCATCTACTTTTGATAGTCATATTTCCAAATCTGAAAATTTTATTTTTGATAGTCATATTTCAATCCAACAACTT[T/A]
TCATCTTAATGACTTTCTTGGATTTAATGCATGACTCTTCATTCTTCCACACAAGATTGGTTGCATGGGCATCGAGAAATGTAAATATTAATGAATCGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.20%	2.60%	2.31%	47.86%	NA
All Indica	2759	27.70%	4.30%	2.39%	65.64%	NA
All Japonica	1512	84.10%	0.10%	0.26%	15.48%	NA
Aus	269	33.80%	0.00%	11.52%	54.65%	NA
Indica I	595	15.80%	0.30%	0.84%	83.03%	NA
Indica II	465	41.50%	0.40%	1.51%	56.56%	NA
Indica III	913	29.80%	9.20%	4.16%	56.85%	NA
Indica Intermediate	786	26.10%	3.80%	2.04%	68.07%	NA
Temperate Japonica	767	92.00%	0.00%	0.13%	7.82%	NA
Tropical Japonica	504	88.90%	0.40%	0.20%	10.52%	NA
Japonica Intermediate	241	49.00%	0.00%	0.83%	50.21%	NA
VI/Aromatic	96	56.20%	3.10%	6.25%	34.38%	NA
Intermediate	90	54.40%	2.20%	2.22%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401777097	A -> DEL	N	N	silent_mutation	Average:30.226; most accessible tissue: Minghui63 flower, score: 57.187	N	N	N	N
vg0401777097	A -> T	LOC_Os04g03884.1	3_prime_UTR_variant ; 253.0bp to feature; MODIFIER	silent_mutation	Average:30.226; most accessible tissue: Minghui63 flower, score: 57.187	N	N	N	N
vg0401777097	A -> T	LOC_Os04g03880.1	upstream_gene_variant ; 3189.0bp to feature; MODIFIER	silent_mutation	Average:30.226; most accessible tissue: Minghui63 flower, score: 57.187	N	N	N	N
vg0401777097	A -> T	LOC_Os04g03890.1	downstream_gene_variant ; 2797.0bp to feature; MODIFIER	silent_mutation	Average:30.226; most accessible tissue: Minghui63 flower, score: 57.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401777097	NA	7.22E-06	mr1919	Ind_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