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Detailed information for vg0412624645:

Variant ID: vg0412624645 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12624645
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTATATTTGTATAGGCAATTAAGAATTTGCTGTTGGGAATAGTCCCACATTGCTTATCTAGGGGGAGTTGAACCAACTTAAAAGTGAGGGGAGCCCCT[C/G]
ATCTCTTGAGCTAGCTTTTGGGGTGTAGCAAGGCTTTCTCCCAGTTGGGCCAACGTCTCCCGGTTTTGGGCCAACAAGTGGTATCAGAGCCAAACCCACA

Reverse complement sequence

TGTGGGTTTGGCTCTGATACCACTTGTTGGCCCAAAACCGGGAGACGTTGGCCCAACTGGGAGAAAGCCTTGCTACACCCCAAAAGCTAGCTCAAGAGAT[G/C]
AGGGGCTCCCCTCACTTTTAAGTTGGTTCAACTCCCCCTAGATAAGCAATGTGGGACTATTCCCAACAGCAAATTCTTAATTGCCTATACAAATATACAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.90%	0.10%	4.68%	55.31%	NA
All Indica	2759	10.40%	0.30%	6.63%	82.71%	NA
All Japonica	1512	95.20%	0.00%	0.20%	4.63%	NA
Aus	269	5.60%	0.00%	11.52%	82.90%	NA
Indica I	595	9.40%	0.70%	5.04%	84.87%	NA
Indica II	465	25.20%	0.40%	8.39%	66.02%	NA
Indica III	913	4.60%	0.00%	4.60%	90.80%	NA
Indica Intermediate	786	9.20%	0.10%	9.16%	81.55%	NA
Temperate Japonica	767	96.70%	0.00%	0.13%	3.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	82.20%	0.00%	0.41%	17.43%	NA
VI/Aromatic	96	91.70%	0.00%	2.08%	6.25%	NA
Intermediate	90	61.10%	0.00%	2.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412624645	C -> DEL	N	N	silent_mutation	Average:20.396; most accessible tissue: Callus, score: 28.925	N	N	N	N
vg0412624645	C -> G	LOC_Os04g22290.1	downstream_gene_variant ; 3238.0bp to feature; MODIFIER	silent_mutation	Average:20.396; most accessible tissue: Callus, score: 28.925	N	N	N	N
vg0412624645	C -> G	LOC_Os04g22290-LOC_Os04g22300	intergenic_region ; MODIFIER	silent_mutation	Average:20.396; most accessible tissue: Callus, score: 28.925	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412624645	1.74E-06	NA	mr1874_2	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