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Detailed information for vg1205322151:

Variant ID: vg1205322151 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5322151
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGTTTGTAATAATGAAACTCAGTTAAGATCAATAAAAGTTAAAGTAATTCTCTGTCCTAAGTAGTTTCCCCGGTTTCTCTTCTTGTGCCCTGCCCAT[G/A]
CCAGATGGTGAATACTCGCAGCAATGGGAATGGTCCCAACAACCCCAATAACAACAACAATGGAGAGAATCCCACTCTGGCCCAAGTTCTTGCTCAACAG

Reverse complement sequence

CTGTTGAGCAAGAACTTGGGCCAGAGTGGGATTCTCTCCATTGTTGTTGTTATTGGGGTTGTTGGGACCATTCCCATTGCTGCGAGTATTCACCATCTGG[C/T]
ATGGGCAGGGCACAAGAAGAGAAACCGGGGAAACTACTTAGGACAGAGAATTACTTTAACTTTTATTGATCTTAACTGAGTTTCATTATTACAAACTAAA

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	45.30%	3.00%	15.49%	36.20%	NA
All Indica	2759	17.10%	4.20%	19.79%	58.90%	NA
All Japonica	1512	94.80%	0.30%	1.98%	2.84%	NA
Aus	269	27.90%	7.80%	53.16%	11.15%	NA
Indica I	595	16.80%	1.50%	11.76%	69.92%	NA
Indica II	465	14.80%	0.60%	13.98%	70.54%	NA
Indica III	913	17.10%	7.70%	26.94%	48.30%	NA
Indica Intermediate	786	18.70%	4.30%	20.99%	55.98%	NA
Temperate Japonica	767	96.30%	0.00%	0.91%	2.74%	NA
Tropical Japonica	504	95.00%	1.00%	2.18%	1.79%	NA
Japonica Intermediate	241	89.60%	0.00%	4.98%	5.39%	NA
VI/Aromatic	96	94.80%	1.00%	4.17%	0.00%	NA
Intermediate	90	74.40%	1.10%	10.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205322151	G -> DEL	N	N	silent_mutation	Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1205322151	G -> A	LOC_Os12g10050.1	upstream_gene_variant ; 5.0bp to feature; MODIFIER	silent_mutation	Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1205322151	G -> A	LOC_Os12g10040.1	downstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:4.947; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg1205322151	G -> A	LOC_Os12g10040-LOC_Os12g10050	intergenic_region ; MODIFIER	silent_mutation	Average:4.947; 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
vg1205322151	4.05E-06	4.66E-07	mr1483_2	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