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Detailed information for vg0114364662:

Variant ID: vg0114364662 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14364662
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCAACCGGGACTAAAGATCCCGGTGATCTTTAGTCCCGGTTGGTAACACCAACCGGGACTACAGTCCCACCCCTTTATATATGTCTTCTTCCTCCTCCA[G/A]
CCCGAGCAAGCTTCAAAATTTCTTCAAAAAAGAGGTGAGGTCATGCCAAAATTTATATTGAATTTACTTTGGTGATTATATACAAATAGGAGGTGCCTAA

Reverse complement sequence

TTAGGCACCTCCTATTTGTATATAATCACCAAAGTAAATTCAATATAAATTTTGGCATGACCTCACCTCTTTTTTGAAGAAATTTTGAAGCTTGCTCGGG[C/T]
TGGAGGAGGAAGAAGACATATATAAAGGGGTGGGACTGTAGTCCCGGTTGGTGTTACCAACCGGGACTAAAGATCACCGGGATCTTTAGTCCCGGTTGGT

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	48.80%	0.30%	12.76%	38.15%	NA
All Indica	2759	23.60%	0.00%	17.69%	58.72%	NA
All Japonica	1512	95.40%	0.90%	2.38%	1.32%	NA
Aus	269	31.60%	0.00%	20.07%	48.33%	NA
Indica I	595	19.20%	0.00%	3.03%	77.82%	NA
Indica II	465	16.30%	0.00%	19.14%	64.52%	NA
Indica III	913	32.40%	0.00%	28.15%	39.43%	NA
Indica Intermediate	786	21.00%	0.00%	15.78%	63.23%	NA
Temperate Japonica	767	92.80%	1.70%	4.56%	0.91%	NA
Tropical Japonica	504	97.80%	0.00%	0.20%	1.98%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	75.00%	0.00%	20.83%	4.17%	NA
Intermediate	90	62.20%	0.00%	5.56%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114364662	G -> A	LOC_Os01g25402.1	upstream_gene_variant ; 518.0bp to feature; MODIFIER	silent_mutation	Average:19.336; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0114364662	G -> A	LOC_Os01g25386-LOC_Os01g25402	intergenic_region ; MODIFIER	silent_mutation	Average:19.336; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0114364662	G -> DEL	N	N	silent_mutation	Average:19.336; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114364662	1.43E-06	NA	mr1100	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
vg0114364662	6.40E-07	NA	mr1613	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
vg0114364662	1.31E-07	1.31E-07	mr1855	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
vg0114364662	2.95E-06	NA	mr1962	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