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Detailed information for vg1124826323:

Variant ID: vg1124826323 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24826323
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATATGACTATCAAAAATAAATTTTTCAGATTTGGAAATATGACTATCAAAAGTAGATGGAGGAAGTATCTCTAACAGGTACCACAATGCTCTCATTATT[T/A]
TTTTTTTGCTTGCTGTCATGAATTTGACATCAATATTTAAGGAGGATGGATTCTGATCGCTTAGGAGGATGTCCACCCACGCTGTTCGTCGTCGATCCTC

Reverse complement sequence

GAGGATCGACGACGAACAGCGTGGGTGGACATCCTCCTAAGCGATCAGAATCCATCCTCCTTAAATATTGATGTCAAATTCATGACAGCAAGCAAAAAAA[A/T]
AATAATGAGAGCATTGTGGTACCTGTTAGAGATACTTCCTCCATCTACTTTTGATAGTCATATTTCCAAATCTGAAAAATTTATTTTTGATAGTCATATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.10%	0.50%	0.40%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.30%	1.50%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	94.90%	2.70%	2.35%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124826323	T -> A	LOC_Os11g41365.1	missense_variant ; p.Lys94Ile; MODERATE	nonsynonymous_codon ; K94I	Average:53.808; most accessible tissue: Zhenshan97 panicle, score: 82.888	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124826323	4.55E-06	4.55E-06	mr1024	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