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Detailed information for vg1126133720:

Variant ID: vg1126133720 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26133720
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

AATGATGATAACAATAAAGAGGGGAGAAGCAATATGCCCGTAAAGAAGTAGGTGGTGGTGATTGATGTGATATCTAAAAGCTATAAACAATACCCCAAAT[T/C]
GAATCCCAATAATAATTAAGAGCAGAGACAACGGGTAGACTGTTAAGCAGCACGGTCATGGCAGTGGCGGGACTTCTAGAAAGTAAAAATTAAATCCCAA

Reverse complement sequence

TTGGGATTTAATTTTTACTTTCTAGAAGTCCCGCCACTGCCATGACCGTGCTGCTTAACAGTCTACCCGTTGTCTCTGCTCTTAATTATTATTGGGATTC[A/G]
ATTTGGGGTATTGTTTATAGCTTTTAGATATCACATCAATCACCACCACCTACTTCTTTACGGGCATATTGCTTCTCCCCTCTTTATTGTTATCATCATT

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	23.50%	21.00%	0.15%	55.29%	NA
All Indica	2759	5.80%	17.40%	0.25%	76.51%	NA
All Japonica	1512	60.00%	25.30%	0.00%	14.75%	NA
Aus	269	2.20%	40.10%	0.00%	57.62%	NA
Indica I	595	6.10%	18.50%	0.34%	75.13%	NA
Indica II	465	6.50%	24.70%	0.22%	68.60%	NA
Indica III	913	3.50%	10.40%	0.11%	85.98%	NA
Indica Intermediate	786	7.90%	20.50%	0.38%	71.25%	NA
Temperate Japonica	767	85.10%	12.00%	0.00%	2.87%	NA
Tropical Japonica	504	23.80%	51.00%	0.00%	25.20%	NA
Japonica Intermediate	241	55.60%	13.70%	0.00%	30.71%	NA
VI/Aromatic	96	15.60%	5.20%	0.00%	79.17%	NA
Intermediate	90	26.70%	20.00%	0.00%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126133720	T -> DEL	N	N	silent_mutation	Average:31.537; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg1126133720	T -> C	LOC_Os11g43310.1	downstream_gene_variant ; 2546.0bp to feature; MODIFIER	silent_mutation	Average:31.537; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N
vg1126133720	T -> C	LOC_Os11g43300-LOC_Os11g43310	intergenic_region ; MODIFIER	silent_mutation	Average:31.537; most accessible tissue: Minghui63 root, score: 56.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126133720	4.36E-06	NA	mr1042_2	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
vg1126133720	1.03E-06	NA	mr1871_2	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