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Detailed information for vg0220182817:

Variant ID: vg0220182817 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20182817
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GGTATGGACCCCAATTCTCACTGTGATGATGACCGCGCTGTTGTAATTGTTTGGTGATCGCGGTTGGATTGAGCAAGTGAGAAGTGCTCATGAAAAATTG[T/C]
ACTATTAAGCAGTTTCAGCACCATACTATCAGTGTGTTAAGCGCCGCTGCTATTTCAATACTAGTATTGATTTTATCTATACAGAGAGAGCACGGTTGTT

Reverse complement sequence

AACAACCGTGCTCTCTCTGTATAGATAAAATCAATACTAGTATTGAAATAGCAGCGGCGCTTAACACACTGATAGTATGGTGCTGAAACTGCTTAATAGT[A/G]
CAATTTTTCATGAGCACTTCTCACTTGCTCAATCCAACCGCGATCACCAAACAATTACAACAGCGCGGTCATCATCACAGTGAGAATTGGGGTCCATACC

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	94.30%	5.70%	0.02%	0.00%	NA
All Indica	2759	95.70%	4.30%	0.00%	0.00%	NA
All Japonica	1512	92.00%	7.90%	0.07%	0.00%	NA
Aus	269	90.70%	9.30%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	93.60%	6.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	3.30%	0.00%	0.00%	NA
Temperate Japonica	767	89.40%	10.40%	0.13%	0.00%	NA
Tropical Japonica	504	94.40%	5.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	5.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0220182817	T -> C	LOC_Os02g33850.1	upstream_gene_variant ; 787.0bp to feature; MODIFIER	silent_mutation	Average:82.123; most accessible tissue: Callus, score: 89.891	N	N	N	N
vg0220182817	T -> C	LOC_Os02g33860.1	intron_variant ; MODIFIER	silent_mutation	Average:82.123; most accessible tissue: Callus, score: 89.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220182817	3.01E-06	NA	mr1768	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
vg0220182817	4.73E-07	NA	mr1172_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