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Detailed information for vg0206815673:

Variant ID: vg0206815673 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6815673
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

CTCAAGAACCTCACCCACTTGGATGTCTCCTACAACAACATATCCTCTCCATTCCCTACAATGCTCTACAATTGCTCCAATCTCAAGTACCTTGACCTTT[C/T]
GAACAACGCCTTTGCTGGGAAGCTCCCAAATGATATAAATAGTCTACCAGCGCTGCTCGAGCATCTCAACCTTTCATCTAATCACTTCACTGGCAGAATT

Reverse complement sequence

AATTCTGCCAGTGAAGTGATTAGATGAAAGGTTGAGATGCTCGAGCAGCGCTGGTAGACTATTTATATCATTTGGGAGCTTCCCAGCAAAGGCGTTGTTC[G/A]
AAAGGTCAAGGTACTTGAGATTGGAGCAATTGTAGAGCATTGTAGGGAATGGAGAGGATATGTTGTTGTAGGAGACATCCAAGTGGGTGAGGTTCTTGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.50%	1.00%	2.73%	7.79%	NA
All Indica	2759	99.90%	0.00%	0.00%	0.14%	NA
All Japonica	1512	65.90%	3.00%	8.13%	22.88%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.00%	0.38%	NA
Temperate Japonica	767	92.00%	0.90%	2.48%	4.56%	NA
Tropical Japonica	504	34.70%	4.80%	14.48%	46.03%	NA
Japonica Intermediate	241	48.10%	6.20%	12.86%	32.78%	NA
VI/Aromatic	96	89.60%	0.00%	1.04%	9.38%	NA
Intermediate	90	84.40%	1.10%	5.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206815673	C -> T	LOC_Os02g12910.1	missense_variant ; p.Ser128Leu; MODERATE	nonsynonymous_codon ; S128L	Average:66.707; most accessible tissue: Minghui63 flag leaf, score: 84.608	possibly damaging	1.746	DELETERIOUS	0.03
vg0206815673	C -> DEL	LOC_Os02g12910.1	N	frameshift_variant	Average:66.707; most accessible tissue: Minghui63 flag leaf, score: 84.608	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206815673	NA	2.92E-13	mr1449	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
vg0206815673	NA	1.88E-09	mr1668	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
vg0206815673	NA	5.51E-10	mr1398_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
vg0206815673	NA	6.00E-06	mr1398_2	Jap_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
vg0206815673	NA	3.73E-16	mr1552_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
vg0206815673	3.75E-07	NA	mr1563_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
vg0206815673	NA	1.18E-06	mr1730_2	Jap_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