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Detailed information for vg1215225435:

Variant ID: vg1215225435 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15225435
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCAGTACTGGATTCCTAAATTTTTATTATCATCTAACCCCAGTACTGAGGCTGAATCAATTTTTATTAGCATCCAAGACTTAATCAATTGTCTTTGCT[A/G]
ATGCTTCTACTAGTGCCGTTGTCGCTACATGTTTGGTTAAGGTAAATGAAAAATTTGAATTAAAGAATGTAGCTTTGGTTAAGGACTTAAAGTACAATTT

Reverse complement sequence

AAATTGTACTTTAAGTCCTTAACCAAAGCTACATTCTTTAATTCAAATTTTTCATTTACCTTAACCAAACATGTAGCGACAACGGCACTAGTAGAAGCAT[T/C]
AGCAAAGACAATTGATTAAGTCTTGGATGCTAATAAAAATTGATTCAGCCTCAGTACTGGGGTTAGATGATAATAAAAATTTAGGAATCCAGTACTGAGA

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	25.80%	15.70%	42.49%	16.08%	NA
All Indica	2759	28.20%	2.00%	51.79%	18.05%	NA
All Japonica	1512	25.80%	44.10%	21.23%	8.86%	NA
Aus	269	6.30%	0.40%	55.39%	37.92%	NA
Indica I	595	9.40%	1.00%	51.76%	37.82%	NA
Indica II	465	56.30%	2.80%	28.60%	12.26%	NA
Indica III	913	22.50%	0.80%	67.80%	8.98%	NA
Indica Intermediate	786	32.40%	3.60%	46.95%	17.05%	NA
Temperate Japonica	767	13.80%	75.60%	9.00%	1.56%	NA
Tropical Japonica	504	41.70%	2.20%	38.29%	17.86%	NA
Japonica Intermediate	241	30.70%	31.50%	24.48%	13.28%	NA
VI/Aromatic	96	11.50%	0.00%	71.88%	16.67%	NA
Intermediate	90	23.30%	21.10%	44.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215225435	A -> DEL	N	N	silent_mutation	Average:8.18; most accessible tissue: Callus, score: 24.058	N	N	N	N
vg1215225435	A -> G	LOC_Os12g26140.1	intron_variant ; MODIFIER	silent_mutation	Average:8.18; most accessible tissue: Callus, score: 24.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215225435	NA	3.49E-06	mr1030	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
vg1215225435	NA	2.93E-06	mr1686	Ind_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
vg1215225435	1.01E-06	1.01E-06	mr1541_2	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