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Detailed information for vg0714301117:

Variant ID: vg0714301117 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14301117
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, C: 0.36, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CACAAGCAACTTAACCCAGATCAAGCCTAGTCCTCCAGATCATCACCTTCACTGAAGTACTCCTCCTCTGATGAATGAATATTGCAAGAATGAGCATATG[C/A]
CATACTTAACAAGCCACACAGCAAATATGCAAGTGCACAGGATAACAAAGGACGGCATAATAAAGTTCATTTGCATAAACAACATTTAATAAATATTTAG

Reverse complement sequence

CTAAATATTTATTAAATGTTGTTTATGCAAATGAACTTTATTATGCCGTCCTTTGTTATCCTGTGCACTTGCATATTTGCTGTGTGGCTTGTTAAGTATG[G/T]
CATATGCTCATTCTTGCAATATTCATTCATCAGAGGAGGAGTACTTCAGTGAAGGTGATGATCTGGAGGACTAGGCTTGATCTGGGTTAAGTTGCTTGTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.20%	0.20%	1.02%	57.64%	NA
All Indica	2759	19.20%	0.30%	1.09%	79.34%	NA
All Japonica	1512	81.90%	0.00%	0.79%	17.26%	NA
Aus	269	15.60%	0.00%	1.86%	82.53%	NA
Indica I	595	41.80%	0.20%	0.50%	57.48%	NA
Indica II	465	20.20%	0.20%	0.86%	78.71%	NA
Indica III	913	2.10%	0.20%	1.42%	96.28%	NA
Indica Intermediate	786	21.50%	0.60%	1.27%	76.59%	NA
Temperate Japonica	767	81.20%	0.00%	1.17%	17.60%	NA
Tropical Japonica	504	93.70%	0.00%	0.00%	6.35%	NA
Japonica Intermediate	241	59.80%	0.00%	1.24%	39.00%	NA
VI/Aromatic	96	82.30%	0.00%	1.04%	16.67%	NA
Intermediate	90	60.00%	0.00%	0.00%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714301117	C -> DEL	N	N	silent_mutation	Average:13.848; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0714301117	C -> A	LOC_Os07g25060.1	upstream_gene_variant ; 2250.0bp to feature; MODIFIER	silent_mutation	Average:13.848; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0714301117	C -> A	LOC_Os07g25070.1	downstream_gene_variant ; 4421.0bp to feature; MODIFIER	silent_mutation	Average:13.848; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0714301117	C -> A	LOC_Os07g25050-LOC_Os07g25060	intergenic_region ; MODIFIER	silent_mutation	Average:13.848; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714301117	NA	1.81E-06	mr1184_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0714301117	NA	1.10E-06	mr1418_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0714301117	2.56E-06	NA	mr1494_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