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Detailed information for vg1226380204:

Variant ID: vg1226380204 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26380204
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CCACCGTTTTAGGGTACCGTATTTTCGTATGGACAGTTTTGCCCTTGCGTTCACATGCTTAGACCTCGAGCTCTGGTCCGGCTCGACCAGCTCGCCATTC[A/G]
TTCCCTACACCGAAACCCTAGCTTCTTGACGGCGGCAAGTTCTTACCAAATTGCCGCATTGTAGCCACCGGCGTCGAGGATTCCTTGCGGTGTTCGAAAT

Reverse complement sequence

ATTTCGAACACCGCAAGGAATCCTCGACGCCGGTGGCTACAATGCGGCAATTTGGTAAGAACTTGCCGCCGTCAAGAAGCTAGGGTTTCGGTGTAGGGAA[T/C]
GAATGGCGAGCTGGTCGAGCCGGACCAGAGCTCGAGGTCTAAGCATGTGAACGCAAGGGCAAAACTGTCCATACGAAAATACGGTACCCTAAAACGGTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.60%	39.30%	3.03%	1.12%	NA
All Indica	2759	58.50%	37.80%	1.78%	1.92%	NA
All Japonica	1512	60.40%	33.90%	5.75%	0.00%	NA
Aus	269	7.10%	92.60%	0.37%	0.00%	NA
Indica I	595	41.20%	56.00%	2.86%	0.00%	NA
Indica II	465	59.10%	33.50%	1.94%	5.38%	NA
Indica III	913	71.20%	25.80%	0.66%	2.30%	NA
Indica Intermediate	786	56.50%	40.50%	2.16%	0.89%	NA
Temperate Japonica	767	64.30%	26.10%	9.65%	0.00%	NA
Tropical Japonica	504	50.80%	47.60%	1.59%	0.00%	NA
Japonica Intermediate	241	68.00%	29.90%	2.07%	0.00%	NA
VI/Aromatic	96	80.20%	18.80%	1.04%	0.00%	NA
Intermediate	90	57.80%	36.70%	5.56%	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
vg1226380204	A -> DEL	N	N	silent_mutation	Average:34.866; most accessible tissue: Callus, score: 79.992	N	N	N	N
vg1226380204	A -> G	LOC_Os12g42450.1	upstream_gene_variant ; 1475.0bp to feature; MODIFIER	silent_mutation	Average:34.866; most accessible tissue: Callus, score: 79.992	N	N	N	N
vg1226380204	A -> G	LOC_Os12g42440.1	downstream_gene_variant ; 355.0bp to feature; MODIFIER	silent_mutation	Average:34.866; most accessible tissue: Callus, score: 79.992	N	N	N	N
vg1226380204	A -> G	LOC_Os12g42460.1	downstream_gene_variant ; 4658.0bp to feature; MODIFIER	silent_mutation	Average:34.866; most accessible tissue: Callus, score: 79.992	N	N	N	N
vg1226380204	A -> G	LOC_Os12g42440-LOC_Os12g42450	intergenic_region ; MODIFIER	silent_mutation	Average:34.866; most accessible tissue: Callus, score: 79.992	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226380204	NA	1.16E-08	mr1715_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