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Detailed information for vg1124662697:

Variant ID: vg1124662697 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24662697
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAGAAAACATCTCTATCCAAGTCAGATGTGTGTAGAAAGTTGGATTGTAATGCACGTGAGGGTTAAGGTGAGAGATCTTAAATTTGAATCCCATATC[C/T]
CACATTTTTTTTTTGACTTTGTATGTGTCGAGGAGTGATACTTATAGACCGGATAATTAGGGTATTGAGGTACGTTGGAATGAGGATATACGTAATTCGA

Reverse complement sequence

TCGAATTACGTATATCCTCATTCCAACGTACCTCAATACCCTAATTATCCGGTCTATAAGTATCACTCCTCGACACATACAAAGTCAAAAAAAAAATGTG[G/A]
GATATGGGATTCAAATTTAAGATCTCTCACCTTAACCCTCACGTGCATTACAATCCAACTTTCTACACACATCTGACTTGGATAGAGATGTTTTCTTTTT

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	86.00%	9.20%	3.07%	1.65%	NA
All Indica	2759	92.50%	1.30%	3.59%	2.61%	NA
All Japonica	1512	72.80%	24.20%	2.71%	0.26%	NA
Aus	269	90.30%	8.90%	0.37%	0.37%	NA
Indica I	595	93.40%	0.00%	5.71%	0.84%	NA
Indica II	465	94.20%	0.00%	3.01%	2.80%	NA
Indica III	913	90.70%	3.30%	1.97%	4.05%	NA
Indica Intermediate	786	92.70%	0.90%	4.20%	2.16%	NA
Temperate Japonica	767	75.70%	18.90%	5.22%	0.13%	NA
Tropical Japonica	504	70.40%	29.40%	0.00%	0.20%	NA
Japonica Intermediate	241	68.50%	30.30%	0.41%	0.83%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	86.70%	8.90%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124662697	C -> T	LOC_Os11g41160.1	upstream_gene_variant ; 3369.0bp to feature; MODIFIER	silent_mutation	Average:67.76; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg1124662697	C -> T	LOC_Os11g41160.2	upstream_gene_variant ; 3446.0bp to feature; MODIFIER	silent_mutation	Average:67.76; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg1124662697	C -> T	LOC_Os11g41160.3	upstream_gene_variant ; 3406.0bp to feature; MODIFIER	silent_mutation	Average:67.76; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg1124662697	C -> T	LOC_Os11g41160-LOC_Os11g41170	intergenic_region ; MODIFIER	silent_mutation	Average:67.76; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg1124662697	C -> DEL	N	N	silent_mutation	Average:67.76; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124662697	4.38E-06	NA	mr1194_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