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Detailed information for vg1106210872:

Variant ID: vg1106210872 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6210872
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GTTACCATGAAAGCTTGTCCCTGGATGATGCAGTACAAACGTTCCAGCAGAGGCAGCTGGTTCCGTCGGCATGGTTGTCACTTGTTCATGCAGTGAATCG[G/A]
TGACCTTGATTGACCTTGGAAGATTAGATAGAGAGGCCATTGTTGTTGCGAAGAAGATGATTGTGATCCGATAATAATGTGCCATATGTAAAGCTTAATC

Reverse complement sequence

GATTAAGCTTTACATATGGCACATTATTATCGGATCACAATCATCTTCTTCGCAACAACAATGGCCTCTCTATCTAATCTTCCAAGGTCAATCAAGGTCA[C/T]
CGATTCACTGCATGAACAAGTGACAACCATGCCGACGGAACCAGCTGCCTCTGCTGGAACGTTTGTACTGCATCATCCAGGGACAAGCTTTCATGGTAAC

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	86.80%	13.20%	0.04%	0.00%	NA
All Indica	2759	81.50%	18.50%	0.04%	0.00%	NA
All Japonica	1512	93.30%	6.70%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	94.60%	5.40%	0.00%	0.00%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	63.10%	36.80%	0.11%	0.00%	NA
Indica Intermediate	786	85.60%	14.40%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	81.90%	18.10%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1106210872	G -> A	LOC_Os11g11220.1	missense_variant ; p.Thr14Ile; MODERATE	nonsynonymous_codon ; T14I	Average:23.081; most accessible tissue: Minghui63 young leaf, score: 31.294	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106210872	2.86E-07	1.29E-06	mr1577_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