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Detailed information for vg0225323727:

Variant ID: vg0225323727 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25323727
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: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGATTAGAGTGCTTGTCAATGGTATTTCATGGATTTTCTCTTTCTTTTTACTAATTTAACTTTCCACCAGACCATCACTCGCTCATTACTGCACATCA[T/C]
CTCGTGTGTGGAGCCCACGTTTGTGTTGGATAAGATTTTCTATGGTTTCTCTAGTCTTGGAGCTTGTGTTTAGTTGGCGATAATTTTATCGTCGGCTTGC

Reverse complement sequence

GCAAGCCGACGATAAAATTATCGCCAACTAAACACAAGCTCCAAGACTAGAGAAACCATAGAAAATCTTATCCAACACAAACGTGGGCTCCACACACGAG[A/G]
TGATGTGCAGTAATGAGCGAGTGATGGTCTGGTGGAAAGTTAAATTAGTAAAAAGAAAGAGAAAATCCATGAAATACCATTGACAAGCACTCTAATCCCA

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	87.90%	11.90%	0.21%	0.00%	NA
All Indica	2759	89.10%	10.50%	0.36%	0.00%	NA
All Japonica	1512	85.00%	15.00%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.30%	0.20%	0.50%	0.00%	NA
Indica II	465	97.60%	2.20%	0.22%	0.00%	NA
Indica III	913	75.20%	24.80%	0.00%	0.00%	NA
Indica Intermediate	786	92.50%	6.70%	0.76%	0.00%	NA
Temperate Japonica	767	95.70%	4.30%	0.00%	0.00%	NA
Tropical Japonica	504	70.60%	29.40%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	19.10%	0.00%	0.00%	NA
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0225323727	T -> C	LOC_Os02g42110.1	downstream_gene_variant ; 2286.0bp to feature; MODIFIER	silent_mutation	Average:58.779; most accessible tissue: Callus, score: 79.569	N	N	N	N
vg0225323727	T -> C	LOC_Os02g42120.1	downstream_gene_variant ; 410.0bp to feature; MODIFIER	silent_mutation	Average:58.779; most accessible tissue: Callus, score: 79.569	N	N	N	N
vg0225323727	T -> C	LOC_Os02g42120-LOC_Os02g42134	intergenic_region ; MODIFIER	silent_mutation	Average:58.779; most accessible tissue: Callus, score: 79.569	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225323727	1.08E-06	NA	mr1446_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
vg0225323727	NA	5.40E-06	mr1446_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
vg0225323727	NA	5.87E-06	mr1623_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