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Detailed information for vg0412453374:

Variant ID: vg0412453374 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12453374
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAAAATGTGTAGAATCCATTAAAAATGGTTTTGTTCTCTGTTTCAGTAGTCTTATAGCCTGTTTGTATTGTTTGCTTTGTATGTCGCTTAGATTCCAG[C/T]
TCTTCCAACGCTCCGGTGTACTTCGAGATAGTCACCGAGGTTCCTCCAGCAGCAGAGCAAGGCAAGTCATGCCTGTCACTTGAACATGTTGATCCTATAT

Reverse complement sequence

ATATAGGATCAACATGTTCAAGTGACAGGCATGACTTGCCTTGCTCTGCTGCTGGAGGAACCTCGGTGACTATCTCGAAGTACACCGGAGCGTTGGAAGA[G/A]
CTGGAATCTAAGCGACATACAAAGCAAACAATACAAACAGGCTATAAGACTACTGAAACAGAGAACAAAACCATTTTTAATGGATTCTACACATTTTTCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.40%	0.40%	12.82%	47.40%	NA
All Indica	2759	8.00%	0.70%	21.31%	70.06%	NA
All Japonica	1512	99.10%	0.00%	0.00%	0.86%	NA
Aus	269	0.70%	0.40%	3.35%	95.54%	NA
Indica I	595	7.10%	0.30%	7.06%	85.55%	NA
Indica II	465	9.50%	0.00%	32.04%	58.49%	NA
Indica III	913	8.30%	1.30%	23.88%	66.48%	NA
Indica Intermediate	786	7.40%	0.50%	22.77%	69.34%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	58.90%	1.10%	10.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412453374	C -> DEL	N	N	silent_mutation	Average:9.206; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N
vg0412453374	C -> T	LOC_Os04g21990.1	upstream_gene_variant ; 490.0bp to feature; MODIFIER	silent_mutation	Average:9.206; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N
vg0412453374	C -> T	LOC_Os04g22000.1	upstream_gene_variant ; 1902.0bp to feature; MODIFIER	silent_mutation	Average:9.206; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N
vg0412453374	C -> T	LOC_Os04g21990-LOC_Os04g22000	intergenic_region ; MODIFIER	silent_mutation	Average:9.206; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412453374	4.84E-06	NA	mr1904	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
vg0412453374	5.26E-07	2.99E-09	mr1904	Ind_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