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Detailed information for vg0618508336:

Variant ID: vg0618508336 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18508336
Reference Allele: T	Alternative Allele: C,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTAGGTAAAAGTGTTTCTAGGAAGGCAAAGAGTGAAATCTTCAACTCGGTATCAGATGCTGCACGGAGTGAAAAGTGCAAGCACCGGTTACCAGGCAA[T/C,G]
ACCATGTCTTGGGAGATGATCCAATGGGAAAGAACACATCAAGGTTAAAGGTGTAAAGGAATACGTTGAATGCTAACTGAGGACAACCTGAAGATAATAA

Reverse complement sequence

TTATTATCTTCAGGTTGTCCTCAGTTAGCATTCAACGTATTCCTTTACACCTTTAACCTTGATGTGTTCTTTCCCATTGGATCATCTCCCAAGACATGGT[A/G,C]
TTGCCTGGTAACCGGTGCTTGCACTTTTCACTCCGTGCAGCATCTGATACCGAGTTGAAGATTTCACTCTTTGCCTTCCTAGAAACACTTTTACCTAGGT

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	39.90%	0.10%	10.05%	49.85%	G: 0.02%
All Indica	2759	16.90%	0.00%	10.51%	72.56%	NA
All Japonica	1512	87.30%	0.30%	4.37%	8.00%	G: 0.07%
Aus	269	8.20%	0.70%	26.02%	65.06%	NA
Indica I	595	26.40%	0.00%	4.37%	69.24%	NA
Indica II	465	17.00%	0.00%	4.09%	78.92%	NA
Indica III	913	9.60%	0.00%	20.81%	69.55%	NA
Indica Intermediate	786	18.20%	0.00%	7.00%	74.81%	NA
Temperate Japonica	767	87.60%	0.40%	1.30%	10.69%	NA
Tropical Japonica	504	86.10%	0.00%	9.52%	4.17%	G: 0.20%
Japonica Intermediate	241	88.80%	0.40%	3.32%	7.47%	NA
VI/Aromatic	96	37.50%	1.00%	37.50%	23.96%	NA
Intermediate	90	46.70%	0.00%	14.44%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618508336	T -> C	LOC_Os06g31860.1	upstream_gene_variant ; 4698.0bp to feature; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> C	LOC_Os06g31850.1	downstream_gene_variant ; 1118.0bp to feature; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> C	LOC_Os06g31850-LOC_Os06g31860	intergenic_region ; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> G	LOC_Os06g31860.1	upstream_gene_variant ; 4698.0bp to feature; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> G	LOC_Os06g31850.1	downstream_gene_variant ; 1118.0bp to feature; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> G	LOC_Os06g31850-LOC_Os06g31860	intergenic_region ; MODIFIER	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N
vg0618508336	T -> DEL	N	N	silent_mutation	Average:5.224; most accessible tissue: Callus, score: 10.784	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618508336	8.45E-08	8.45E-08	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