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Detailed information for vg1124756886:

Variant ID: vg1124756886 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24756886
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, G: 0.48, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCGTCCTCGCGGCGCGGTCGCCGGTGTTCAGGGCGGAGCTCCTCGGCCCCATGAGGGAGCACGCCGCGACGACCATCCGCGTCGACGACATGGACGCC[T/G]
CCGTGTTCGCCGCTCTGCTGCGCTTCGTCTACACCGACGAGCTGCCGGAGCTGGACGGCGGCAGCGCGGCGGCGATGGCGCAGCACCTGCTGGTGGCGGC

Reverse complement sequence

GCCGCCACCAGCAGGTGCTGCGCCATCGCCGCCGCGCTGCCGCCGTCCAGCTCCGGCAGCTCGTCGGTGTAGACGAAGCGCAGCAGAGCGGCGAACACGG[A/C]
GGCGTCCATGTCGTCGACGCGGATGGTCGTCGCGGCGTGCTCCCTCATGGGGCCGAGGAGCTCCGCCCTGAACACCGGCGACCGCGCCGCGAGGACGCAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.50%	30.10%	0.08%	0.38%	NA
All Indica	2759	86.40%	12.90%	0.07%	0.54%	NA
All Japonica	1512	36.20%	63.60%	0.00%	0.20%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	75.10%	23.70%	0.00%	1.18%	NA
Indica II	465	91.60%	7.70%	0.00%	0.65%	NA
Indica III	913	91.30%	8.10%	0.22%	0.33%	NA
Indica Intermediate	786	86.30%	13.50%	0.00%	0.25%	NA
Temperate Japonica	767	15.40%	84.50%	0.00%	0.13%	NA
Tropical Japonica	504	59.90%	39.90%	0.00%	0.20%	NA
Japonica Intermediate	241	52.70%	46.90%	0.00%	0.41%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	2.22%	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
vg1124756886	T -> DEL	LOC_Os11g41300.1	N	frameshift_variant	Average:74.205; most accessible tissue: Minghui63 flag leaf, score: 84.791	N	N	N	N
vg1124756886	T -> G	LOC_Os11g41300.1	missense_variant ; p.Ser241Ala; MODERATE	nonsynonymous_codon ; S241A	Average:74.205; most accessible tissue: Minghui63 flag leaf, score: 84.791	benign	-0.086	TOLERATED	0.50

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124756886	NA	1.73E-06	mr1543	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1124756886	NA	5.67E-08	mr1871	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251