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Detailed information for vg1014025113:

Variant ID: vg1014025113 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14025113
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.14, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

GGAAATGACCTGAAGCCAGGTGCCACCTACTAGGCGCCGGTGCTTGTACTCCCCGCCTCCCGTCGCCCATCATCTGAACCGAGCCGAGGCGGCAGCTCCC[T/C]
GGCCGCCACGCTCCGCCTCGCTCCTTCCCACCTCTCTCTCGCCGTTGCTTCCCAGATCCAGCGGAGCCCCAATGCCGAGGCGGCGCAGGACTAGGCGAGG

Reverse complement sequence

CCTCGCCTAGTCCTGCGCCGCCTCGGCATTGGGGCTCCGCTGGATCTGGGAAGCAACGGCGAGAGAGAGGTGGGAAGGAGCGAGGCGGAGCGTGGCGGCC[A/G]
GGGAGCTGCCGCCTCGGCTCGGTTCAGATGATGGGCGACGGGAGGCGGGGAGTACAAGCACCGGCGCCTAGTAGGTGGCACCTGGCTTCAGGTCATTTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.00%	39.90%	0.11%	0.00%	NA
All Indica	2759	42.60%	57.20%	0.18%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	58.80%	41.20%	0.00%	0.00%	NA
Indica II	465	37.80%	61.70%	0.43%	0.00%	NA
Indica III	913	35.50%	64.40%	0.11%	0.00%	NA
Indica Intermediate	786	41.30%	58.40%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014025113	T -> C	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:63.363; most accessible tissue: Minghui63 young leaf, score: 77.654	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014025113	NA	2.12E-07	mr1162	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
vg1014025113	NA	6.30E-08	mr1577	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
vg1014025113	NA	5.26E-07	mr1577	Ind_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
vg1014025113	NA	1.99E-07	mr1587	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
vg1014025113	NA	4.22E-09	mr1722	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
vg1014025113	NA	5.31E-06	mr1780	Ind_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
vg1014025113	1.32E-06	6.35E-07	mr1792	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
vg1014025113	5.35E-06	4.03E-08	mr1792	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
vg1014025113	NA	1.47E-07	mr1803	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