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Detailed information for vg0424937526:

Variant ID: vg0424937526 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 24937526
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGTTAGTAAAGACACACATTCTACAGTTTAGAACTATGAGGAACCCACTCTTTTCAATATTCATTTCCCCAAGACCCCAACTAGTGATTTCTTTCAACT[A/G]
TCTAGGCAATACAGTTAGTCATTCAGGCAAAATACCTTGCTGTTCCGAGCACATGAATTTTCATCGGTCACAAGAATTATCCGATCCCCACCTTCAGACC

Reverse complement sequence

GGTCTGAAGGTGGGGATCGGATAATTCTTGTGACCGATGAAAATTCATGTGCTCGGAACAGCAAGGTATTTTGCCTGAATGACTAACTGTATTGCCTAGA[T/C]
AGTTGAAAGAAATCACTAGTTGGGGTCTTGGGGAAATGAATATTGAAAAGAGTGGGTTCCTCATAGTTCTAAACTGTAGAATGTGTGTCTTTACTAACTG

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	57.70%	4.50%	2.29%	35.46%	NA
All Indica	2759	30.80%	6.50%	3.01%	59.66%	NA
All Japonica	1512	99.30%	0.10%	0.07%	0.53%	NA
Aus	269	79.90%	10.80%	8.92%	0.37%	NA
Indica I	595	39.80%	1.20%	1.51%	57.48%	NA
Indica II	465	14.20%	3.20%	3.23%	79.35%	NA
Indica III	913	26.90%	11.60%	4.38%	57.06%	NA
Indica Intermediate	786	38.30%	6.60%	2.42%	52.67%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	98.40%	0.20%	0.20%	1.19%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	73.30%	3.30%	0.00%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0424937526	A -> DEL	N	N	silent_mutation	Average:15.254; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0424937526	A -> G	LOC_Os04g42130.1	upstream_gene_variant ; 2935.0bp to feature; MODIFIER	silent_mutation	Average:15.254; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0424937526	A -> G	LOC_Os04g42110.1	downstream_gene_variant ; 1448.0bp to feature; MODIFIER	silent_mutation	Average:15.254; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0424937526	A -> G	LOC_Os04g42120.1	intron_variant ; MODIFIER	silent_mutation	Average:15.254; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0424937526	NA	2.07E-06	mr1412	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