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Detailed information for vg1106502558:

Variant ID: vg1106502558 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6502558
Reference Allele: A	Alternative Allele: C,G
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

CACTAGCATGTAAAGCCAGCAAAGCTGCTTAATGTGCATCTTCAAATTTACCCAACCAAATTCTGCCTTGGAACCGAATGACCCCATTAAGTAGAGAGAA[A/C,G]
TGCTCAACACCAGTCGGATTCAAAATCAATTGTGCCAATAGTTGCTTTGCCTCATCATCCTGTTCATACCGCTCTACCACTATTTCCAACCATTTGGGCC

Reverse complement sequence

GGCCCAAATGGTTGGAAATAGTGGTAGAGCGGTATGAACAGGATGATGAGGCAAAGCAACTATTGGCACAATTGATTTTGAATCCGACTGGTGTTGAGCA[T/G,C]
TTCTCTCTACTTAATGGGGTCATTCGGTTCCAAGGCAGAATTTGGTTGGGTAAATTTGAAGATGCACATTAAGCAGCTTTGCTGGCTTTACATGCTAGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.50%	36.00%	3.45%	6.03%	NA
All Indica	2759	33.10%	57.70%	5.40%	3.81%	NA
All Japonica	1512	87.10%	1.60%	0.53%	10.78%	NA
Aus	269	82.20%	17.50%	0.37%	0.00%	NA
Indica I	595	27.40%	68.10%	4.20%	0.34%	NA
Indica II	465	23.90%	66.90%	7.96%	1.29%	NA
Indica III	913	39.40%	47.50%	4.93%	8.11%	NA
Indica Intermediate	786	35.60%	56.10%	5.34%	2.93%	NA
Temperate Japonica	767	96.20%	0.80%	0.52%	2.48%	NA
Tropical Japonica	504	73.00%	2.80%	0.79%	23.41%	NA
Japonica Intermediate	241	87.60%	1.70%	0.00%	10.79%	NA
VI/Aromatic	96	84.40%	2.10%	4.17%	9.38%	NA
Intermediate	90	50.00%	40.00%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106502558	A -> DEL	N	N	silent_mutation	Average:49.714; most accessible tissue: Callus, score: 64.49	N	N	N	N
vg1106502558	A -> G	LOC_Os11g11694.1	5_prime_UTR_variant ; 3637.0bp to feature; MODIFIER	N	Average:49.714; most accessible tissue: Callus, score: 64.49	N	N	N	N
vg1106502558	A -> C	LOC_Os11g11694.1	5_prime_UTR_variant ; 3637.0bp to feature; MODIFIER	silent_mutation	Average:49.714; most accessible tissue: Callus, score: 64.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106502558	1.91E-06	NA	mr1263_2	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