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Detailed information for vg1213423613:

Variant ID: vg1213423613 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13423613
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, A: 0.37, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATAAATGGCCCTTCCCATAAAGGGGATAACTTGTGCCGATCCCGTGTAGTTTGAATTTTCCTCAAAACCAGGTCGCCGACTAAGAAAGCACGCGATC[A/G]
GACGTTACGATTGTGATAACGACGCAACCCTTGCAAGTATCGGGCCGACTGAATTAAGGCTGCTTCGCGGGCCTCTTCCAGTCGGTGTAGGTCAACCACT

Reverse complement sequence

AGTGGTTGACCTACACCGACTGGAAGAGGCCCGCGAAGCAGCCTTAATTCAGTCGGCCCGATACTTGCAAGGGTTGCGTCGTTATCACAATCGTAACGTC[T/C]
GATCGCGTGCTTTCTTAGTCGGCGACCTGGTTTTGAGGAAAATTCAAACTACACGGGATCGGCACAAGTTATCCCCTTTATGGGAAGGGCCATTTATAAT

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	45.80%	30.20%	12.97%	11.05%	NA
All Indica	2759	46.50%	38.10%	15.26%	0.14%	NA
All Japonica	1512	51.50%	5.00%	10.12%	33.47%	NA
Aus	269	14.90%	74.00%	11.15%	0.00%	NA
Indica I	595	51.40%	23.20%	25.38%	0.00%	NA
Indica II	465	54.00%	33.10%	12.90%	0.00%	NA
Indica III	913	37.20%	50.80%	11.94%	0.00%	NA
Indica Intermediate	786	49.00%	37.70%	12.85%	0.51%	NA
Temperate Japonica	767	83.80%	4.80%	1.96%	9.39%	NA
Tropical Japonica	504	8.90%	6.30%	17.46%	67.26%	NA
Japonica Intermediate	241	37.30%	2.50%	20.75%	39.42%	NA
VI/Aromatic	96	11.50%	77.10%	5.21%	6.25%	NA
Intermediate	90	61.10%	27.80%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213423613	A -> DEL	N	N	silent_mutation	Average:23.386; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg1213423613	A -> G	LOC_Os12g23640.1	downstream_gene_variant ; 529.0bp to feature; MODIFIER	silent_mutation	Average:23.386; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg1213423613	A -> G	LOC_Os12g23650.1	downstream_gene_variant ; 784.0bp to feature; MODIFIER	silent_mutation	Average:23.386; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg1213423613	A -> G	LOC_Os12g23660.1	downstream_gene_variant ; 2416.0bp to feature; MODIFIER	silent_mutation	Average:23.386; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N
vg1213423613	A -> G	LOC_Os12g23640-LOC_Os12g23650	intergenic_region ; MODIFIER	silent_mutation	Average:23.386; most accessible tissue: Minghui63 flag leaf, score: 48.324	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213423613	NA	3.27E-06	mr1509_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
vg1213423613	4.12E-06	7.46E-14	mr1722_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