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Detailed information for vg1121357584:

Variant ID: vg1121357584 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21357584
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTTTACCGAGTTCAAACTTGTATGCCACTTCCGCCTTCGGGATTGATGCGCTTCCAATCAACTGATCCATAGTTAGACCGGTGTCCGAAATGAATTCC[G/A]
TTATGCCAAATTCTTCGCCGGTCACCAACGGCTCGACCTCTTGGTTTGGTTGTTCTCCAAGCTGAGGGACTAGTTTGGACTTCTTGTAATAGGCTTTCTT

Reverse complement sequence

AAGAAAGCCTATTACAAGAAGTCCAAACTAGTCCCTCAGCTTGGAGAACAACCAAACCAAGAGGTCGAGCCGTTGGTGACCGGCGAAGAATTTGGCATAA[C/T]
GGAATTCATTTCGGACACCGGTCTAACTATGGATCAGTTGATTGGAAGCGCATCAATCCCGAAGGCGGAAGTGGCATACAAGTTTGAACTCGGTAAACCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.20%	5.80%	0.74%	15.26%	NA
All Indica	2759	75.00%	0.30%	0.87%	23.85%	NA
All Japonica	1512	79.80%	17.10%	0.40%	2.71%	NA
Aus	269	92.60%	0.00%	1.12%	6.32%	NA
Indica I	595	76.60%	0.00%	0.67%	22.69%	NA
Indica II	465	65.20%	0.00%	0.22%	34.62%	NA
Indica III	913	79.70%	0.10%	1.42%	18.73%	NA
Indica Intermediate	786	74.00%	0.90%	0.76%	24.30%	NA
Temperate Japonica	767	89.40%	6.40%	0.52%	3.65%	NA
Tropical Japonica	504	71.20%	26.60%	0.40%	1.79%	NA
Japonica Intermediate	241	66.80%	31.50%	0.00%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	5.60%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121357584	G -> A	LOC_Os11g36280.1	missense_variant ; p.Thr1510Met; MODERATE	nonsynonymous_codon ; T1510M	Average:26.048; most accessible tissue: Minghui63 flag leaf, score: 54.348	unknown	unknown	DELETERIOUS	0.03
vg1121357584	G -> DEL	LOC_Os11g36280.1	N	frameshift_variant	Average:26.048; most accessible tissue: Minghui63 flag leaf, score: 54.348	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121357584	1.57E-06	NA	mr1691	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