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Detailed information for vg0406139947:

Variant ID: vg0406139947 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6139947
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TGTACAACATCGGGTTGAGTTGATATGCTTCAAGATGATTGCCGCACGTGGATAGAGTCCTGAGAAGGCAATTGTATCTATTAATTAGGATATTTTATGT[A/G]
ATTTCCTTAGAGATATGCTTGGGCAAAAGTCTGCCGCAAAGACTTATGGTATCTTAGAGTTTGTTAGAGATAATAGTCGTGTCCGTTATGGACATATCTT

Reverse complement sequence

AAGATATGTCCATAACGGACACGACTATTATCTCTAACAAACTCTAAGATACCATAAGTCTTTGCGGCAGACTTTTGCCCAAGCATATCTCTAAGGAAAT[T/C]
ACATAAAATATCCTAATTAATAGATACAATTGCCTTCTCAGGACTCTATCCACGTGCGGCAATCATCTTGAAGCATATCAACTCAACCCGATGTTGTACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.70%	2.10%	6.12%	2.12%	NA
All Indica	2759	83.70%	3.40%	9.57%	3.26%	NA
All Japonica	1512	99.10%	0.10%	0.79%	0.00%	NA
Aus	269	93.30%	0.40%	3.35%	2.97%	NA
Indica I	595	94.10%	1.50%	3.36%	1.01%	NA
Indica II	465	74.80%	1.10%	21.72%	2.37%	NA
Indica III	913	83.70%	4.40%	7.01%	4.93%	NA
Indica Intermediate	786	81.20%	5.20%	10.05%	3.56%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.20%	0.20%	1.59%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	1.10%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406139947	A -> DEL	N	N	silent_mutation	Average:25.532; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0406139947	A -> G	LOC_Os04g11240.1	upstream_gene_variant ; 1255.0bp to feature; MODIFIER	silent_mutation	Average:25.532; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0406139947	A -> G	LOC_Os04g11230.1	intron_variant ; MODIFIER	silent_mutation	Average:25.532; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406139947	3.58E-06	NA	mr1913	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