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Detailed information for vg1225934717:

Variant ID: vg1225934717 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 25934717
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCCATTGCATTCATCATCTACTTTTTTAAATCTGATATTAATAATTATTTAAAAATAGATTTACTTTAAAATAAACGGACGAAGTTAAAACTTAACTT[A/G]
GAGCTTGTTTGGGGGAGTTTCCAACAACCGAAGATTCTTCTAAAACCTACCGTTGCCAGAAACTCCCCCAAACAGTCCAGATTTTCACACAGTTTTTAAG

Reverse complement sequence

CTTAAAAACTGTGTGAAAATCTGGACTGTTTGGGGGAGTTTCTGGCAACGGTAGGTTTTAGAAGAATCTTCGGTTGTTGGAAACTCCCCCAAACAAGCTC[T/C]
AAGTTAAGTTTTAACTTCGTCCGTTTATTTTAAAGTAAATCTATTTTTAAATAATTATTAATATCAGATTTAAAAAAGTAGATGATGAATGCAATGGAAG

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	94.80%	5.00%	0.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	84.10%	15.20%	0.73%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	79.80%	19.20%	1.04%	0.00%	NA
Tropical Japonica	504	96.40%	3.60%	0.00%	0.00%	NA
Japonica Intermediate	241	71.80%	27.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	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
vg1225934717	A -> G	LOC_Os12g41860-LOC_Os12g41870	intergenic_region ; MODIFIER	silent_mutation	Average:38.022; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1225934717	NA	5.56E-06	mr1070	Jap_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
vg1225934717	NA	2.13E-06	mr1097	Jap_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
vg1225934717	1.95E-06	1.95E-06	mr1128	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