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Detailed information for vg0114943457:

Variant ID: vg0114943457 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14943457
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTACCCTGTCGAACAACCGCGGTTCGACAGGGATACCTATCGAACAACCACAGTTCGACAAGTACATGTCGAACTGCGTCAGTTCGACAGGGTAGGTG[G/A]
TCCAAAAACAAATAAAAAATTACATGAACAGTATCACTACAATGCTAGGCAGGGACATATCGAACAACCAAAGTTCGATAGGGTTGCGTGAACAGCGCGC

Reverse complement sequence

GCGCGCTGTTCACGCAACCCTATCGAACTTTGGTTGTTCGATATGTCCCTGCCTAGCATTGTAGTGATACTGTTCATGTAATTTTTTATTTGTTTTTGGA[C/T]
CACCTACCCTGTCGAACTGACGCAGTTCGACATGTACTTGTCGAACTGTGGTTGTTCGATAGGTATCCCTGTCGAACCGCGGTTGTTCGACAGGGTACTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.40%	1.30%	0.74%	57.55%	NA
All Indica	2759	8.40%	2.20%	1.23%	88.11%	NA
All Japonica	1512	98.70%	0.00%	0.00%	1.32%	NA
Aus	269	35.30%	0.00%	0.00%	64.68%	NA
Indica I	595	16.60%	0.00%	1.18%	82.18%	NA
Indica II	465	5.60%	10.80%	1.08%	82.58%	NA
Indica III	913	3.30%	0.10%	1.20%	95.40%	NA
Indica Intermediate	786	9.80%	1.40%	1.40%	87.40%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	97.00%	0.00%	0.00%	2.98%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	40.60%	0.00%	0.00%	59.38%	NA
Intermediate	90	56.70%	0.00%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114943457	G -> A	LOC_Os01g26340.1	downstream_gene_variant ; 4.0bp to feature; MODIFIER	silent_mutation	Average:11.69; most accessible tissue: Callus, score: 27.349	N	N	N	N
vg0114943457	G -> A	LOC_Os01g26350.1	downstream_gene_variant ; 4119.0bp to feature; MODIFIER	silent_mutation	Average:11.69; most accessible tissue: Callus, score: 27.349	N	N	N	N
vg0114943457	G -> A	LOC_Os01g26340-LOC_Os01g26350	intergenic_region ; MODIFIER	silent_mutation	Average:11.69; most accessible tissue: Callus, score: 27.349	N	N	N	N
vg0114943457	G -> DEL	N	N	silent_mutation	Average:11.69; most accessible tissue: Callus, score: 27.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114943457	4.72E-06	NA	mr1530_2	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