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Detailed information for vg0115380845:

Variant ID: vg0115380845 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15380845
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGTTCTAGTTCCACTCTTGTGCAATATTGTTCTAGCAATTTTTAGACTCAAATGAGTAGATGTGAAAATTTTTGGATGCTTGAACTTGTGGGAGGAGG[T/C]
CTGCCCGGAGACACAGGCGGTCTGACTGTGGGTCAGCCGCCGGTCTGACCGGCGTGTGCGCGCGGTTTGACCGGCCGTCAGTCGTCGGTCTGACCGGCCA

Reverse complement sequence

TGGCCGGTCAGACCGACGACTGACGGCCGGTCAAACCGCGCGCACACGCCGGTCAGACCGGCGGCTGACCCACAGTCAGACCGCCTGTGTCTCCGGGCAG[A/G]
CCTCCTCCCACAAGTTCAAGCATCCAAAAATTTTCACATCTACTCATTTGAGTCTAAAAATTGCTAGAACAATATTGCACAAGAGTGGAACTAGAACATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.80%	1.30%	6.26%	33.71%	NA
All Indica	2759	44.00%	1.80%	9.53%	44.65%	NA
All Japonica	1512	85.60%	0.10%	0.33%	13.96%	NA
Aus	269	61.30%	3.00%	8.55%	27.14%	NA
Indica I	595	24.90%	1.70%	10.59%	62.86%	NA
Indica II	465	35.10%	0.90%	11.18%	52.90%	NA
Indica III	913	63.70%	2.70%	8.98%	24.53%	NA
Indica Intermediate	786	40.70%	1.50%	8.40%	49.36%	NA
Temperate Japonica	767	94.50%	0.00%	0.00%	5.48%	NA
Tropical Japonica	504	89.10%	0.20%	0.40%	10.32%	NA
Japonica Intermediate	241	50.20%	0.00%	1.24%	48.55%	NA
VI/Aromatic	96	45.80%	0.00%	0.00%	54.17%	NA
Intermediate	90	66.70%	0.00%	5.56%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115380845	T -> DEL	N	N	silent_mutation	Average:13.278; most accessible tissue: Callus, score: 29.742	N	N	N	N
vg0115380845	T -> C	LOC_Os01g27560.1	upstream_gene_variant ; 256.0bp to feature; MODIFIER	silent_mutation	Average:13.278; most accessible tissue: Callus, score: 29.742	N	N	N	N
vg0115380845	T -> C	LOC_Os01g27550.1	downstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:13.278; most accessible tissue: Callus, score: 29.742	N	N	N	N
vg0115380845	T -> C	LOC_Os01g27570.1	downstream_gene_variant ; 4052.0bp to feature; MODIFIER	silent_mutation	Average:13.278; most accessible tissue: Callus, score: 29.742	N	N	N	N
vg0115380845	T -> C	LOC_Os01g27550-LOC_Os01g27560	intergenic_region ; MODIFIER	silent_mutation	Average:13.278; most accessible tissue: Callus, score: 29.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115380845	3.38E-06	6.91E-06	mr1576_2	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