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Detailed information for vg1126651130:

Variant ID: vg1126651130 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26651130
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.23, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTCCCTTCGCGCCAGCCGATCGACGTTTCTTCGACTGAGGAGCCGACTACAGGGGGCAGCCAGGCCGACGAGGAGTAGAGGAGGCAGTCTTCAGCAGC[T/C]
GTCCGTGTGTTAGGCCCTTTTGTTCCGCCGCCAACTCTTTTGGAGTCGTGGCGAGGTAGCGCGTGCGTGTGTTTGTTGTGGGTGTTGTTTGGTAGTCTGG

Reverse complement sequence

CCAGACTACCAAACAACACCCACAACAAACACACGCACGCGCTACCTCGCCACGACTCCAAAAGAGTTGGCGGCGGAACAAAAGGGCCTAACACACGGAC[A/G]
GCTGCTGAAGACTGCCTCCTCTACTCCTCGTCGGCCTGGCTGCCCCCTGTAGTCGGCTCCTCAGTCGAAGAAACGTCGATCGGCTGGCGCGAAGGGACCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.70%	4.90%	4.08%	4.32%	NA
All Indica	2759	92.60%	7.10%	0.18%	0.04%	NA
All Japonica	1512	72.80%	1.70%	12.24%	13.29%	NA
Aus	269	98.10%	0.70%	1.12%	0.00%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	86.40%	12.90%	0.55%	0.11%	NA
Indica Intermediate	786	95.40%	4.60%	0.00%	0.00%	NA
Temperate Japonica	767	85.30%	3.40%	6.26%	5.08%	NA
Tropical Japonica	504	57.90%	0.00%	20.44%	21.63%	NA
Japonica Intermediate	241	63.90%	0.00%	14.11%	21.99%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126651130	T -> DEL	N	N	silent_mutation	Average:35.204; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1126651130	T -> C	LOC_Os11g44150.1	upstream_gene_variant ; 503.0bp to feature; MODIFIER	silent_mutation	Average:35.204; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1126651130	T -> C	LOC_Os11g44140.1	downstream_gene_variant ; 21.0bp to feature; MODIFIER	silent_mutation	Average:35.204; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N
vg1126651130	T -> C	LOC_Os11g44140-LOC_Os11g44150	intergenic_region ; MODIFIER	silent_mutation	Average:35.204; most accessible tissue: Minghui63 flag leaf, score: 76.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126651130	3.31E-06	3.31E-06	mr1573	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