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Detailed information for vg0714102413:

Variant ID: vg0714102413 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14102413
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCTGTTCATGGCGTAAAGTGGACATTAAACTGGCTCAGCTCGACTACCCATTTCGCAATGCGGCTGACAACGTCTTTGTTTCTCACGACTTCACCGAG[G/A]
GGGAAGGAGGAGATAACTGTGACTCTGTGGGCTTGAAAGTAGTGGCGTAGCTTCCTTGATGTCATGATGACCGCGTAAAGTAGCTTTTGGATCTGTGGAT

Reverse complement sequence

ATCCACAGATCCAAAAGCTACTTTACGCGGTCATCATGACATCAAGGAAGCTACGCCACTACTTTCAAGCCCACAGAGTCACAGTTATCTCCTCCTTCCC[C/T]
CTCGGTGAAGTCGTGAGAAACAAAGACGTTGTCAGCCGCATTGCGAAATGGGTAGTCGAGCTGAGCCAGTTTAATGTCCACTTTACGCCATGAACAGCCA

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	41.50%	0.50%	19.72%	38.28%	NA
All Indica	2759	17.60%	0.70%	24.57%	57.16%	NA
All Japonica	1512	85.40%	0.00%	1.85%	12.70%	NA
Aus	269	20.10%	1.50%	74.35%	4.09%	NA
Indica I	595	36.60%	0.20%	18.32%	44.87%	NA
Indica II	465	15.30%	0.00%	11.83%	72.90%	NA
Indica III	913	2.60%	1.30%	36.58%	59.47%	NA
Indica Intermediate	786	22.00%	0.60%	22.90%	54.45%	NA
Temperate Japonica	767	86.80%	0.00%	1.17%	11.99%	NA
Tropical Japonica	504	93.10%	0.00%	0.40%	6.55%	NA
Japonica Intermediate	241	65.10%	0.00%	7.05%	27.80%	NA
VI/Aromatic	96	82.30%	0.00%	13.54%	4.17%	NA
Intermediate	90	56.70%	1.10%	14.44%	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
vg0714102413	G -> DEL	N	N	silent_mutation	Average:8.029; most accessible tissue: Callus, score: 14.657	N	N	N	N
vg0714102413	G -> A	LOC_Os07g24820.1	upstream_gene_variant ; 4242.0bp to feature; MODIFIER	silent_mutation	Average:8.029; most accessible tissue: Callus, score: 14.657	N	N	N	N
vg0714102413	G -> A	LOC_Os07g24800.1	downstream_gene_variant ; 2748.0bp to feature; MODIFIER	silent_mutation	Average:8.029; most accessible tissue: Callus, score: 14.657	N	N	N	N
vg0714102413	G -> A	LOC_Os07g24810.1	intron_variant ; MODIFIER	silent_mutation	Average:8.029; most accessible tissue: Callus, score: 14.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714102413	1.66E-06	1.03E-06	mr1344	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