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Detailed information for vg1126752035:

Variant ID: vg1126752035 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26752035
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGTTTCGGTGTTGTGATGCTGGAGGTATTGACGGGGAAGAAACCATATCTCTTTAAAGAAGAATGGAAGGAGGAGAAGAGAGAAAAATGTGAGCAAGA[T/G]
GGAAAGAACACAGAAGAGGACAAGGAGGAGAGTGAACGAGAAGAAGAGGAGAAGACAACAGAAGAACAACATGAGTGGCAAAAGCGGGACGGGTGGTCTA

Reverse complement sequence

TAGACCACCCGTCCCGCTTTTGCCACTCATGTTGTTCTTCTGTTGTCTTCTCCTCTTCTTCTCGTTCACTCTCCTCCTTGTCCTCTTCTGTGTTCTTTCC[A/C]
TCTTGCTCACATTTTTCTCTCTTCTCCTCCTTCCATTCTTCTTTAAAGAGATATGGTTTCTTCCCCGTCAATACCTCCAGCATCACAACACCGAAACTGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.70%	8.40%	2.24%	53.66%	NA
All Indica	2759	25.90%	10.10%	3.59%	60.35%	NA
All Japonica	1512	56.30%	6.00%	0.20%	37.50%	NA
Aus	269	24.90%	7.10%	0.00%	68.03%	NA
Indica I	595	47.20%	9.60%	8.07%	35.13%	NA
Indica II	465	28.00%	4.50%	2.15%	65.38%	NA
Indica III	913	5.90%	16.20%	1.97%	75.90%	NA
Indica Intermediate	786	31.80%	6.90%	2.93%	58.40%	NA
Temperate Japonica	767	80.30%	5.20%	0.13%	14.34%	NA
Tropical Japonica	504	26.60%	4.60%	0.40%	68.45%	NA
Japonica Intermediate	241	42.30%	11.20%	0.00%	46.47%	NA
VI/Aromatic	96	19.80%	2.10%	2.08%	76.04%	NA
Intermediate	90	35.60%	8.90%	2.22%	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
vg1126752035	T -> DEL	LOC_Os11g44260.1	N	frameshift_variant	Average:55.988; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg1126752035	T -> G	LOC_Os11g44260.1	missense_variant ; p.Asp252Glu; MODERATE	nonsynonymous_codon ; D252E	Average:55.988; most accessible tissue: Minghui63 panicle, score: 85.556	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126752035	4.65E-06	1.89E-10	mr1010_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