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Detailed information for vg1219382346:

Variant ID: vg1219382346 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19382346
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CCATGGACGTGTGATCTTCAGGGATGTGATCGATTATGTGGACTGAACCACCTAATAACATCCAAACTTGTGTACATTCCAATGACTTCATCTAGATTTG[A/G]
CCGAAAGCATGAATCATCACCACCATTAGGACAACTACAGGAGTGCAAGCGGAAGCTCAACATTTTTAGTTTAGGTGATGTATACTCATATGTAGGCAAT

Reverse complement sequence

ATTGCCTACATATGAGTATACATCACCTAAACTAAAAATGTTGAGCTTCCGCTTGCACTCCTGTAGTTGTCCTAATGGTGGTGATGATTCATGCTTTCGG[T/C]
CAAATCTAGATGAAGTCATTGGAATGTACACAAGTTTGGATGTTATTAGGTGGTTCAGTCCACATAATCGATCACATCCCTGAAGATCACACGTCCATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.10%	37.20%	6.62%	0.99%	NA
All Indica	2759	83.80%	5.80%	9.79%	0.62%	NA
All Japonica	1512	2.40%	95.20%	0.40%	1.92%	NA
Aus	269	81.80%	6.70%	11.52%	0.00%	NA
Indica I	595	75.50%	7.10%	17.31%	0.17%	NA
Indica II	465	91.80%	4.50%	3.01%	0.65%	NA
Indica III	913	86.20%	2.50%	10.30%	0.99%	NA
Indica Intermediate	786	82.40%	9.50%	7.51%	0.51%	NA
Temperate Japonica	767	1.40%	98.40%	0.13%	0.00%	NA
Tropical Japonica	504	1.80%	92.10%	0.40%	5.75%	NA
Japonica Intermediate	241	7.10%	91.70%	1.24%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	27.80%	64.40%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219382346	A -> DEL	N	N	silent_mutation	Average:8.862; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1219382346	A -> G	LOC_Os12g32130.1	downstream_gene_variant ; 55.0bp to feature; MODIFIER	silent_mutation	Average:8.862; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1219382346	A -> G	LOC_Os12g32140.1	downstream_gene_variant ; 1576.0bp to feature; MODIFIER	silent_mutation	Average:8.862; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1219382346	A -> G	LOC_Os12g32130-LOC_Os12g32140	intergenic_region ; MODIFIER	silent_mutation	Average:8.862; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219382346	1.36E-06	NA	mr1308	Ind_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