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Detailed information for vg1106670187:

Variant ID: vg1106670187 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6670187
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.62, T: 0.38, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTGATTCATTGTTAAATATAATTTCATGTACACATATAGTTTTACATATTTCATAAATTATTTTAATAAGACGAACGGTCAAACATGTGGTAAAAAGT[C/T]
AAAAGTGTCAAATATTTTGAAACGGAGGGATTACTTTGCAGTTGCAGATTTGCAGCCGCCGCGGCCGGCAGCGAGGCGCGGATGCGACCGACGGAGTGAG

Reverse complement sequence

CTCACTCCGTCGGTCGCATCCGCGCCTCGCTGCCGGCCGCGGCGGCTGCAAATCTGCAACTGCAAAGTAATCCCTCCGTTTCAAAATATTTGACACTTTT[G/A]
ACTTTTTACCACATGTTTGACCGTTCGTCTTATTAAAATAATTTATGAAATATGTAAAACTATATGTGTACATGAAATTATATTTAACAATGAATCAAAT

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	36.40%	27.10%	0.99%	35.44%	NA
All Indica	2759	42.30%	6.20%	1.27%	50.27%	NA
All Japonica	1512	17.70%	66.60%	0.26%	15.48%	NA
Aus	269	91.10%	1.90%	0.37%	6.69%	NA
Indica I	595	22.40%	2.70%	1.68%	73.28%	NA
Indica II	465	27.30%	1.50%	0.65%	70.54%	NA
Indica III	913	60.10%	11.20%	1.10%	27.60%	NA
Indica Intermediate	786	45.40%	5.90%	1.53%	47.20%	NA
Temperate Japonica	767	24.10%	72.00%	0.13%	3.78%	NA
Tropical Japonica	504	6.50%	63.10%	0.40%	29.96%	NA
Japonica Intermediate	241	20.30%	56.80%	0.41%	22.41%	NA
VI/Aromatic	96	10.40%	76.00%	2.08%	11.46%	NA
Intermediate	90	36.70%	30.00%	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
vg1106670187	C -> T	LOC_Os11g12000.1	intron_variant ; MODIFIER	silent_mutation	Average:16.202; most accessible tissue: Callus, score: 81.863	N	N	N	N
vg1106670187	C -> DEL	N	N	silent_mutation	Average:16.202; most accessible tissue: Callus, score: 81.863	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106670187	2.90E-06	2.12E-06	mr1567_2	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