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Detailed information for vg0713719162:

Variant ID: vg0713719162 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13719162
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.43, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAGTTGCATGCTTGGAGCTGTTTGCAACAAATAAGTCTGGCCTTGTTTGGTTGGGGAAAAATTTTGGGTTTGGTTGTCACATCGGATATACGGACACA[C/T]
ATTTGAAGTATTAAATGTAGTCTAATAACTATAAAAATTACAGATTCCGCTAGGAAAATGAAAGATGAATTTATTAGGCCTAATTAAGAGTAGTGATATA

Reverse complement sequence

TATATCACTACTCTTAATTAGGCCTAATAAATTCATCTTTCATTTTCCTAGCGGAATCTGTAATTTTTATAGTTATTAGACTACATTTAATACTTCAAAT[G/A]
TGTGTCCGTATATCCGATGTGACAACCAAACCCAAAATTTTTCCCCAACCAAACAAGGCCAGACTTATTTGTTGCAAACAGCTCCAAGCATGCAACTCCT

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	29.90%	26.40%	1.27%	42.45%	NA
All Indica	2759	40.80%	1.50%	1.78%	55.93%	NA
All Japonica	1512	2.40%	68.70%	0.46%	28.44%	NA
Aus	269	77.70%	21.60%	0.00%	0.74%	NA
Indica I	595	59.80%	0.80%	1.34%	37.98%	NA
Indica II	465	16.80%	2.80%	3.01%	77.42%	NA
Indica III	913	41.40%	0.70%	1.64%	56.30%	NA
Indica Intermediate	786	39.90%	2.20%	1.53%	56.36%	NA
Temperate Japonica	767	1.00%	61.50%	0.52%	36.90%	NA
Tropical Japonica	504	4.00%	92.10%	0.00%	3.97%	NA
Japonica Intermediate	241	3.70%	42.30%	1.24%	52.70%	NA
VI/Aromatic	96	24.00%	74.00%	1.04%	1.04%	NA
Intermediate	90	21.10%	42.20%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713719162	C -> DEL	N	N	silent_mutation	Average:13.073; most accessible tissue: Callus, score: 45.928	N	N	N	N
vg0713719162	C -> T	LOC_Os07g24150-LOC_Os07g24160	intergenic_region ; MODIFIER	silent_mutation	Average:13.073; most accessible tissue: Callus, score: 45.928	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713719162	NA	1.60E-07	mr1559	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
vg0713719162	NA	9.76E-15	mr1592	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
vg0713719162	NA	3.02E-26	mr1888	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
vg0713719162	NA	4.36E-06	mr1095_2	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
vg0713719162	NA	2.07E-20	mr1146_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
vg0713719162	NA	9.84E-13	mr1217_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
vg0713719162	NA	1.21E-10	mr1222_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
vg0713719162	NA	1.01E-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
vg0713719162	NA	2.28E-09	mr1506_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
vg0713719162	NA	1.90E-07	mr1683_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
vg0713719162	NA	7.02E-07	mr1824_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
vg0713719162	NA	4.71E-13	mr1838_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
vg0713719162	NA	1.77E-19	mr1922_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
vg0713719162	NA	6.96E-12	mr1986_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