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Detailed information for vg1110170506:

Variant ID: vg1110170506 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10170506
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGTGATCTGCAGATTTTTATCTGTAGATTAATTGAAGATGCACATGAGAAATGCTTGATTAGGCCTGGTGTTATGGTGCTGAATTGCTGATTGAAAAAA[C/T]
GGTGATATTGTTGGTATCGTTTTGGTATCAGTTGACATTCCAGAAAGGTTGCAAGCTTATTTCTATTATGTTGACTTAATACTCGCAGGCAGATGTTGTT

Reverse complement sequence

AACAACATCTGCCTGCGAGTATTAAGTCAACATAATAGAAATAAGCTTGCAACCTTTCTGGAATGTCAACTGATACCAAAACGATACCAACAATATCACC[G/A]
TTTTTTCAATCAGCAATTCAGCACCATAACACCAGGCCTAATCAAGCATTTCTCATGTGCATCTTCAATTAATCTACAGATAAAAATCTGCAGATCACCA

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	62.90%	3.70%	2.48%	30.89%	NA
All Indica	2759	46.40%	5.90%	3.77%	43.86%	NA
All Japonica	1512	98.60%	0.00%	0.13%	1.26%	NA
Aus	269	18.20%	3.70%	2.97%	75.09%	NA
Indica I	595	66.90%	4.90%	3.36%	24.87%	NA
Indica II	465	13.50%	1.30%	4.09%	81.08%	NA
Indica III	913	49.40%	9.20%	4.49%	36.91%	NA
Indica Intermediate	786	46.90%	5.70%	3.05%	44.27%	NA
Temperate Japonica	767	98.00%	0.00%	0.13%	1.83%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	67.80%	2.20%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110170506	C -> T	LOC_Os11g18080.1	upstream_gene_variant ; 359.0bp to feature; MODIFIER	silent_mutation	Average:29.614; most accessible tissue: Callus, score: 67.583	N	N	N	N
vg1110170506	C -> T	LOC_Os11g18080-LOC_Os11g18100	intergenic_region ; MODIFIER	silent_mutation	Average:29.614; most accessible tissue: Callus, score: 67.583	N	N	N	N
vg1110170506	C -> DEL	N	N	silent_mutation	Average:29.614; most accessible tissue: Callus, score: 67.583	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110170506	3.18E-06	3.00E-07	mr1912	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