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Detailed information for vg0115087314:

Variant ID: vg0115087314 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15087314
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACAAGTTTGGTGAACGATTTGAGAGCCACAACTTAGACCAAAAAACATGTGGCAAAGTAGTTCATGAGCACATAACTTCTTATGGCAAGCTAATATGT[G/A]
GTAAGCAAACAAACAATATGCTAACTACCTGTGGCGCGTCAAACTTGAGGCGCCGCAAACTGTGGCACCTATCAAACAGGCCCTTACCAACACCAGAAGT

Reverse complement sequence

ACTTCTGGTGTTGGTAAGGGCCTGTTTGATAGGTGCCACAGTTTGCGGCGCCTCAAGTTTGACGCGCCACAGGTAGTTAGCATATTGTTTGTTTGCTTAC[C/T]
ACATATTAGCTTGCCATAAGAAGTTATGTGCTCATGAACTACTTTGCCACATGTTTTTTGGTCTAAGTTGTGGCTCTCAAATCGTTCACCAAACTTGTGG

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	31.70%	4.00%	3.75%	60.56%	NA
All Indica	2759	8.00%	0.20%	2.36%	89.45%	NA
All Japonica	1512	72.80%	12.00%	6.88%	8.27%	NA
Aus	269	33.80%	0.00%	0.74%	65.43%	NA
Indica I	595	3.70%	0.00%	2.02%	94.29%	NA
Indica II	465	17.60%	0.00%	1.08%	81.29%	NA
Indica III	913	3.40%	0.40%	3.61%	92.55%	NA
Indica Intermediate	786	10.90%	0.10%	1.91%	87.02%	NA
Temperate Japonica	767	90.70%	3.10%	1.43%	4.69%	NA
Tropical Japonica	504	59.10%	27.00%	6.55%	7.34%	NA
Japonica Intermediate	241	44.40%	9.10%	24.90%	21.58%	NA
VI/Aromatic	96	40.60%	0.00%	1.04%	58.33%	NA
Intermediate	90	50.00%	3.30%	5.56%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115087314	G -> A	LOC_Os01g27040.1	upstream_gene_variant ; 4009.0bp to feature; MODIFIER	silent_mutation	Average:8.445; most accessible tissue: Callus, score: 34.835	N	N	N	N
vg0115087314	G -> A	LOC_Os01g27050.1	downstream_gene_variant ; 269.0bp to feature; MODIFIER	silent_mutation	Average:8.445; most accessible tissue: Callus, score: 34.835	N	N	N	N
vg0115087314	G -> A	LOC_Os01g27050-LOC_Os01g27060	intergenic_region ; MODIFIER	silent_mutation	Average:8.445; most accessible tissue: Callus, score: 34.835	N	N	N	N
vg0115087314	G -> DEL	N	N	silent_mutation	Average:8.445; most accessible tissue: Callus, score: 34.835	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115087314	NA	2.83E-08	mr1295	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