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Detailed information for vg0224382266:

Variant ID: vg0224382266 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24382266
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

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

Flanking Sequence (100 bp) in Reference Genome:

GTGTTAGGTTTGGATCTAAGTTGAATGGCCCTTCAACCACAAGAGACCCCTCCCAAGATTCTGAAAGATCAGGGATGGGAAACTTCATTTGTCTGAGAAT[T/C]
TGCTTCTCCCATGTCTCCTCCCTATCAGCTGCATAATAAGGGTTCCCGTCTTCATACCTAAACCCATCGCCGTATTTCATGAAAATGTTCCTTCCATTGC

Reverse complement sequence

GCAATGGAAGGAACATTTTCATGAAATACGGCGATGGGTTTAGGTATGAAGACGGGAACCCTTATTATGCAGCTGATAGGGAGGAGACATGGGAGAAGCA[A/G]
ATTCTCAGACAAATGAAGTTTCCCATCCCTGATCTTTCAGAATCTTGGGAGGGGTCTCTTGTGGTTGAAGGGCCATTCAACTTAGATCCAAACCTAACAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.80%	4.80%	0.55%	2.79%	NA
All Indica	2759	94.20%	1.80%	0.40%	3.55%	NA
All Japonica	1512	88.20%	9.70%	0.86%	1.26%	NA
Aus	269	85.90%	9.70%	0.37%	4.09%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	89.00%	2.20%	1.08%	7.74%	NA
Indica III	913	93.20%	2.10%	0.44%	4.27%	NA
Indica Intermediate	786	94.30%	2.50%	0.25%	2.93%	NA
Temperate Japonica	767	88.70%	9.80%	1.04%	0.52%	NA
Tropical Japonica	504	87.50%	9.30%	0.60%	2.58%	NA
Japonica Intermediate	241	88.40%	10.00%	0.83%	0.83%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	90.00%	5.60%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224382266	T -> DEL	LOC_Os02g40270.1	N	frameshift_variant	Average:57.829; most accessible tissue: Callus, score: 79.631	N	N	N	N
vg0224382266	T -> C	LOC_Os02g40270.1	synonymous_variant ; p.Gln136Gln; LOW	synonymous_codon	Average:57.829; most accessible tissue: Callus, score: 79.631	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224382266	NA	7.47E-07	mr1080	Ind_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
vg0224382266	NA	6.29E-06	mr1150	Ind_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
vg0224382266	NA	4.73E-07	mr1619_2	Ind_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
vg0224382266	4.25E-06	6.74E-08	mr1795_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