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Detailed information for vg0315259700:

Variant ID: vg0315259700 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15259700
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGGTTTTGATAGTAGCACCTCGGCCATATAAGGACCGATCTTCGGGCCTCTGTTGCAAAGCACTACCGTACTTCCACATGTCTAGTGGGTAAGGCTT[T/A]
GTTTGTGGCTCAGTCTGGTTATAAACAAAAGTATACGGATGGAGATGGACGAAGTCGGGGGTCGATGGACATCTCTAGGACAAATGAAGGCTACACGAGC

Reverse complement sequence

GCTCGTGTAGCCTTCATTTGTCCTAGAGATGTCCATCGACCCCCGACTTCGTCCATCTCCATCCGTATACTTTTGTTTATAACCAGACTGAGCCACAAAC[A/T]
AAGCCTTACCCACTAGACATGTGGAAGTACGGTAGTGCTTTGCAACAGAGGCCCGAAGATCGGTCCTTATATGGCCGAGGTGCTACTATCAAAACCATGC

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	36.70%	8.30%	20.23%	34.81%	NA
All Indica	2759	26.30%	8.10%	27.11%	38.53%	NA
All Japonica	1512	62.40%	5.60%	3.84%	28.24%	NA
Aus	269	5.60%	0.40%	50.56%	43.49%	NA
Indica I	595	49.70%	6.40%	13.95%	29.92%	NA
Indica II	465	30.30%	3.70%	14.41%	51.61%	NA
Indica III	913	7.10%	12.60%	45.35%	34.94%	NA
Indica Intermediate	786	28.40%	6.70%	23.41%	41.48%	NA
Temperate Japonica	767	92.70%	1.80%	0.13%	5.35%	NA
Tropical Japonica	504	28.20%	7.70%	9.33%	54.76%	NA
Japonica Intermediate	241	37.30%	12.90%	4.15%	45.64%	NA
VI/Aromatic	96	9.40%	77.10%	3.12%	10.42%	NA
Intermediate	90	45.60%	11.10%	12.22%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315259700	T -> A	LOC_Os03g26750.1	upstream_gene_variant ; 119.0bp to feature; MODIFIER	silent_mutation	Average:7.702; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0315259700	T -> A	LOC_Os03g26730.1	downstream_gene_variant ; 3537.0bp to feature; MODIFIER	silent_mutation	Average:7.702; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0315259700	T -> A	LOC_Os03g26730-LOC_Os03g26750	intergenic_region ; MODIFIER	silent_mutation	Average:7.702; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0315259700	T -> DEL	N	N	silent_mutation	Average:7.702; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315259700	3.55E-06	NA	mr1193_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