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Detailed information for vg1126252287:

Variant ID: vg1126252287 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26252287
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTTACATCATATATATGTGCATGCAAAGCACAGAAGTGTTGTCAGAGCTAAATGTGAGGAAGATGATAGTAGGTTGACGCAGGGCTGCGTTTAGTTCCAT[C/T]
CAAAGTTTGGATTTTGGTTGAAATTGGAGATGATGTGACTGAAAAGTTGTGTGTGTGTATGACAGGTTGATGTGATGGAATTTTGCAAACTTTGGATCCA

Reverse complement sequence

TGGATCCAAAGTTTGCAAAATTCCATCACATCAACCTGTCATACACACACACAACTTTTCAGTCACATCATCTCCAATTTCAACCAAAATCCAAACTTTG[G/A]
ATGGAACTAAACGCAGCCCTGCGTCAACCTACTATCATCTTCCTCACATTTAGCTCTGACAACACTTCTGTGCTTTGCATGCACATATATATGATGTAAA

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	47.40%	6.30%	0.57%	45.70%	NA
All Indica	2759	47.80%	10.00%	0.54%	41.65%	NA
All Japonica	1512	38.00%	0.50%	0.79%	60.65%	NA
Aus	269	82.50%	2.60%	0.00%	14.87%	NA
Indica I	595	32.30%	23.90%	0.50%	43.36%	NA
Indica II	465	63.40%	1.10%	1.29%	34.19%	NA
Indica III	913	47.40%	8.00%	0.11%	44.47%	NA
Indica Intermediate	786	50.80%	7.10%	0.64%	41.48%	NA
Temperate Japonica	767	45.50%	0.00%	1.04%	53.46%	NA
Tropical Japonica	504	21.20%	0.60%	0.60%	77.58%	NA
Japonica Intermediate	241	49.40%	2.10%	0.41%	48.13%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	52.20%	7.80%	0.00%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126252287	C -> T	LOC_Os11g43470.1	upstream_gene_variant ; 1133.0bp to feature; MODIFIER	silent_mutation	Average:47.24; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N
vg1126252287	C -> T	LOC_Os11g43480.1	upstream_gene_variant ; 1675.0bp to feature; MODIFIER	silent_mutation	Average:47.24; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N
vg1126252287	C -> T	LOC_Os11g43470-LOC_Os11g43480	intergenic_region ; MODIFIER	silent_mutation	Average:47.24; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N
vg1126252287	C -> DEL	N	N	silent_mutation	Average:47.24; most accessible tissue: Zhenshan97 root, score: 86.14	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126252287	4.72E-07	NA	mr1191_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1126252287	3.47E-06	NA	mr1191_2	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