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Detailed information for vg1224510581:

Variant ID: vg1224510581 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24510581
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAAATGAAATGGTGAGGCTGCATTAGACAAAGCAAGTAATCTGGTTAATCCTTACTTATATGAAGGCTGCATATAGACGCATGAACAGATTCATAGCCT[G/A]
CCAAGACATTACACTGAATAGCATGACAAGATAGGCACTCAAATTGGCATTGTAGTGCATAGAAACAAGCAGAATAAAGCATAATAACTGATCAAATTAA

Reverse complement sequence

TTAATTTGATCAGTTATTATGCTTTATTCTGCTTGTTTCTATGCACTACAATGCCAATTTGAGTGCCTATCTTGTCATGCTATTCAGTGTAATGTCTTGG[C/T]
AGGCTATGAATCTGTTCATGCGTCTATATGCAGCCTTCATATAAGTAAGGATTAACCAGATTACTTGCTTTGTCTAATGCAGCCTCACCATTTCATTTGT

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	93.70%	4.70%	1.21%	0.40%	NA
All Indica	2759	98.00%	0.00%	1.49%	0.51%	NA
All Japonica	1512	86.20%	13.20%	0.60%	0.07%	NA
Aus	269	96.70%	0.00%	1.86%	1.49%	NA
Indica I	595	93.40%	0.00%	5.38%	1.18%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.90%	0.00%	0.00%	0.11%	NA
Indica Intermediate	786	98.10%	0.10%	1.15%	0.64%	NA
Temperate Japonica	767	98.40%	1.20%	0.39%	0.00%	NA
Tropical Japonica	504	79.20%	20.20%	0.60%	0.00%	NA
Japonica Intermediate	241	61.80%	36.50%	1.24%	0.41%	NA
VI/Aromatic	96	74.00%	25.00%	1.04%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg1224510581	G -> DEL	N	N	silent_mutation	Average:35.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1224510581	G -> A	LOC_Os12g39690.1	downstream_gene_variant ; 3863.0bp to feature; MODIFIER	silent_mutation	Average:35.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1224510581	G -> A	LOC_Os12g39700.1	downstream_gene_variant ; 4003.0bp to feature; MODIFIER	silent_mutation	Average:35.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg1224510581	G -> A	LOC_Os12g39690-LOC_Os12g39700	intergenic_region ; MODIFIER	silent_mutation	Average:35.69; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224510581	2.30E-06	3.13E-08	mr1177	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