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Detailed information for vg0713275136:

Variant ID: vg0713275136 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13275136
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AATTGGACTTAGCCTAGTACATTGTCCCACTATATGAAAGACTGTTGGTTGGCTCACTAGGAGCAGGATTGGGGTGAACGCATGCGTAAGGAGGTTGGGG[G/A]
CATGGTTCACAACGGTGGAACCCGTGAAAGCAGCGACCATGTAGCCTTGCCTAGGCCTGGCAAGTGCCCGACTGCTAGGACGGATCAATATCCCACTCGT

Reverse complement sequence

ACGAGTGGGATATTGATCCGTCCTAGCAGTCGGGCACTTGCCAGGCCTAGGCAAGGCTACATGGTCGCTGCTTTCACGGGTTCCACCGTTGTGAACCATG[C/T]
CCCCAACCTCCTTACGCATGCGTTCACCCCAATCCTGCTCCTAGTGAGCCAACCAACAGTCTTTCATATAGTGGGACAATGTACTAGGCTAAGTCCAATT

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	61.90%	4.10%	10.43%	23.51%	NA
All Indica	2759	62.30%	2.70%	11.63%	23.38%	NA
All Japonica	1512	68.90%	1.60%	5.69%	23.81%	NA
Aus	269	17.80%	32.30%	25.65%	24.16%	NA
Indica I	595	55.60%	0.80%	18.99%	24.54%	NA
Indica II	465	56.60%	3.90%	12.26%	27.31%	NA
Indica III	913	70.30%	3.30%	5.37%	21.03%	NA
Indica Intermediate	786	61.50%	2.70%	12.98%	22.90%	NA
Temperate Japonica	767	66.40%	0.70%	3.13%	29.86%	NA
Tropical Japonica	504	82.30%	3.00%	6.94%	7.74%	NA
Japonica Intermediate	241	49.00%	1.70%	11.20%	38.17%	NA
VI/Aromatic	96	65.60%	7.30%	10.42%	16.67%	NA
Intermediate	90	60.00%	4.40%	7.78%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713275136	G -> DEL	N	N	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275136	G -> A	LOC_Os07g23485.1	3_prime_UTR_variant ; 1964.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275136	G -> A	LOC_Os07g23480.1	upstream_gene_variant ; 3634.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0713275136	G -> A	LOC_Os07g23494.1	downstream_gene_variant ; 1078.0bp to feature; MODIFIER	silent_mutation	Average:20.762; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713275136	1.76E-06	6.90E-08	mr1882_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