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Detailed information for vg1122668782:

Variant ID: vg1122668782 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22668782
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTCACAATTGACGTCCTTCAGGGAATTTAGAGAGAAGATGGATGTGATGCAGATATTCTTTTAAAAGGTTGAATCAAATTGTGATATAGAATAGACAA[C/T]
GGTACAAATATAATTTTCCCTTTTGAAAATAAGCAGGATTGATCCTTCGACACTACTTTAAAAAATCTAATAGGGTTGATGGGAGCCGTTTGTAAATGAA

Reverse complement sequence

TTCATTTACAAACGGCTCCCATCAACCCTATTAGATTTTTTAAAGTAGTGTCGAAGGATCAATCCTGCTTATTTTCAAAAGGGAAAATTATATTTGTACC[G/A]
TTGTCTATTCTATATCACAATTTGATTCAACCTTTTAAAAGAATATCTGCATCACATCCATCTTCTCTCTAAATTCCCTGAAGGACGTCAATTGTGAACA

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	89.50%	1.50%	3.39%	5.65%	NA
All Indica	2759	89.40%	2.10%	4.60%	3.91%	NA
All Japonica	1512	91.00%	0.60%	1.06%	7.34%	NA
Aus	269	77.70%	0.70%	4.83%	16.73%	NA
Indica I	595	85.40%	0.70%	2.18%	11.76%	NA
Indica II	465	82.40%	4.30%	12.47%	0.86%	NA
Indica III	913	95.10%	0.90%	1.53%	2.52%	NA
Indica Intermediate	786	90.10%	3.20%	5.34%	1.40%	NA
Temperate Japonica	767	86.00%	0.90%	1.04%	11.99%	NA
Tropical Japonica	504	97.40%	0.00%	0.40%	2.18%	NA
Japonica Intermediate	241	93.40%	0.80%	2.49%	3.32%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	92.20%	2.20%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122668782	C -> T	LOC_Os11g38270.1	upstream_gene_variant ; 3787.0bp to feature; MODIFIER	silent_mutation	Average:42.954; most accessible tissue: Minghui63 flower, score: 60.203	N	N	N	N
vg1122668782	C -> T	LOC_Os11g38280.1	upstream_gene_variant ; 2491.0bp to feature; MODIFIER	silent_mutation	Average:42.954; most accessible tissue: Minghui63 flower, score: 60.203	N	N	N	N
vg1122668782	C -> T	LOC_Os11g38300.1	downstream_gene_variant ; 3894.0bp to feature; MODIFIER	silent_mutation	Average:42.954; most accessible tissue: Minghui63 flower, score: 60.203	N	N	N	N
vg1122668782	C -> T	LOC_Os11g38280-LOC_Os11g38300	intergenic_region ; MODIFIER	silent_mutation	Average:42.954; most accessible tissue: Minghui63 flower, score: 60.203	N	N	N	N
vg1122668782	C -> DEL	N	N	silent_mutation	Average:42.954; most accessible tissue: Minghui63 flower, score: 60.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122668782	1.87E-06	1.87E-06	mr1164	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