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Detailed information for vg0208626738:

Variant ID: vg0208626738 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8626738
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

CGAACGCTCAAAGGGTGACAATGTTATAATATGTATGGTAAATTGAAAATGAATTAAATTTACCGACCAATGTTCTGTGTATGAGCGTCTTCTCTCTTAA[T/C]
GACTTCGATCGGTCAGTTTGTAGAGTTATACACTCTCCCTAGCCCCCAGCCTTGTCGTCGGAGAATCGTTCTCAGAGGATAAGGCTCTTGGACCCTTGAC

Reverse complement sequence

GTCAAGGGTCCAAGAGCCTTATCCTCTGAGAACGATTCTCCGACGACAAGGCTGGGGGCTAGGGAGAGTGTATAACTCTACAAACTGACCGATCGAAGTC[A/G]
TTAAGAGAGAAGACGCTCATACACAGAACATTGGTCGGTAAATTTAATTCATTTTCAATTTACCATACATATTATAACATTGTCACCCTTTGAGCGTTCG

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	24.00%	13.40%	4.30%	58.27%	NA
All Indica	2759	8.70%	14.40%	7.07%	69.84%	NA
All Japonica	1512	56.50%	0.90%	0.00%	42.53%	NA
Aus	269	3.70%	70.30%	1.12%	24.91%	NA
Indica I	595	15.50%	7.70%	7.73%	69.08%	NA
Indica II	465	6.00%	14.80%	8.82%	70.32%	NA
Indica III	913	0.90%	19.90%	5.81%	73.38%	NA
Indica Intermediate	786	14.40%	12.60%	7.00%	66.03%	NA
Temperate Japonica	767	81.50%	0.30%	0.00%	18.25%	NA
Tropical Japonica	504	28.80%	1.60%	0.00%	69.64%	NA
Japonica Intermediate	241	35.30%	1.70%	0.00%	63.07%	NA
VI/Aromatic	96	1.00%	22.90%	0.00%	76.04%	NA
Intermediate	90	30.00%	15.60%	5.56%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208626738	T -> DEL	N	N	silent_mutation	Average:19.919; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0208626738	T -> C	LOC_Os02g15420.1	intron_variant ; MODIFIER	silent_mutation	Average:19.919; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208626738	6.38E-06	6.38E-06	mr1286_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
vg0208626738	1.93E-06	1.93E-06	mr1427_2	Jap_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
vg0208626738	8.92E-06	NA	mr1665_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
vg0208626738	3.22E-06	4.06E-06	mr1976_2	Jap_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