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Detailed information for vg1204336548:

Variant ID: vg1204336548 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4336548
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTACAATGATTTTATATATATAGGAGTGTTCCACTAGAATAATTAAATTAACATTTATAACTTTCATCGAGTCTCTCATGGGATGGATTCACTCATGT[A/G]
AAATAATTTGTCATGCAAATAAATTGAACTTTATATATAAAATAGGTTTATGTGAGTGTTTAATTAAACATTTAGGTCAATATTGTACCAAGTATCAATT

Reverse complement sequence

AATTGATACTTGGTACAATATTGACCTAAATGTTTAATTAAACACTCACATAAACCTATTTTATATATAAAGTTCAATTTATTTGCATGACAAATTATTT[T/C]
ACATGAGTGAATCCATCCCATGAGAGACTCGATGAAAGTTATAAATGTTAATTTAATTATTCTAGTGGAACACTCCTATATATATAAAATCATTGTAGTG

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	64.50%	0.40%	2.03%	33.11%	NA
All Indica	2759	67.00%	0.50%	2.43%	30.08%	NA
All Japonica	1512	59.00%	0.30%	1.26%	39.48%	NA
Aus	269	82.50%	0.00%	2.23%	15.24%	NA
Indica I	595	60.50%	0.00%	2.18%	37.31%	NA
Indica II	465	64.10%	0.20%	2.58%	33.12%	NA
Indica III	913	73.20%	0.40%	2.85%	23.55%	NA
Indica Intermediate	786	66.50%	1.00%	2.04%	30.41%	NA
Temperate Japonica	767	81.70%	0.00%	0.13%	18.12%	NA
Tropical Japonica	504	33.50%	0.80%	2.98%	62.70%	NA
Japonica Intermediate	241	39.80%	0.00%	1.24%	58.92%	NA
VI/Aromatic	96	27.10%	0.00%	3.12%	69.79%	NA
Intermediate	90	65.60%	0.00%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204336548	A -> DEL	N	N	silent_mutation	Average:7.87; most accessible tissue: Callus, score: 19.655	N	N	N	N
vg1204336548	A -> G	LOC_Os12g08550.1	3_prime_UTR_variant ; 458.0bp to feature; MODIFIER	silent_mutation	Average:7.87; most accessible tissue: Callus, score: 19.655	N	N	N	N
vg1204336548	A -> G	LOC_Os12g08564.1	upstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:7.87; most accessible tissue: Callus, score: 19.655	N	N	N	N
vg1204336548	A -> G	LOC_Os12g08564.3	upstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:7.87; most accessible tissue: Callus, score: 19.655	N	N	N	N
vg1204336548	A -> G	LOC_Os12g08564.4	upstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:7.87; most accessible tissue: Callus, score: 19.655	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204336548	5.56E-07	NA	mr1750	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