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Detailed information for vg0224543759:

Variant ID: vg0224543759 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24543759
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

GCGTGGCCCCCAAATAGAAACGAAAGCAATCTAATCTAGTCTAATATTCTCCTTCTATCTTCCTCATGCGCATCTTCTGCTTCCTTCTTCTTCACGCGCA[C/T]
ATGCACGGCAAAAACAAACACACACAAGGATCGGCAAACTCTAGATGCAACTCAAGAACTCAAAACTAACCGACAGAAACTTCTGAAAACTACAAAAATA

Reverse complement sequence

TATTTTTGTAGTTTTCAGAAGTTTCTGTCGGTTAGTTTTGAGTTCTTGAGTTGCATCTAGAGTTTGCCGATCCTTGTGTGTGTTTGTTTTTGCCGTGCAT[G/A]
TGCGCGTGAAGAAGAAGGAAGCAGAAGATGCGCATGAGGAAGATAGAAGGAGAATATTAGACTAGATTAGATTGCTTTCGTTTCTATTTGGGGGCCACGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.60%	1.70%	3.47%	38.21%	NA
All Indica	2759	38.10%	0.20%	4.13%	57.56%	NA
All Japonica	1512	92.10%	4.40%	1.98%	1.52%	NA
Aus	269	33.80%	0.00%	5.20%	60.97%	NA
Indica I	595	20.50%	0.00%	3.70%	75.80%	NA
Indica II	465	34.80%	0.00%	4.95%	60.22%	NA
Indica III	913	49.10%	0.20%	3.94%	46.77%	NA
Indica Intermediate	786	40.60%	0.50%	4.20%	54.71%	NA
Temperate Japonica	767	91.00%	5.30%	2.74%	0.91%	NA
Tropical Japonica	504	94.80%	2.60%	0.60%	1.98%	NA
Japonica Intermediate	241	89.60%	5.40%	2.49%	2.49%	NA
VI/Aromatic	96	77.10%	8.30%	1.04%	13.54%	NA
Intermediate	90	74.40%	0.00%	5.56%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224543759	C -> T	LOC_Os02g40470.1	upstream_gene_variant ; 1063.0bp to feature; MODIFIER	silent_mutation	Average:45.105; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N
vg0224543759	C -> T	LOC_Os02g40480.1	downstream_gene_variant ; 1686.0bp to feature; MODIFIER	silent_mutation	Average:45.105; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N
vg0224543759	C -> T	LOC_Os02g40470-LOC_Os02g40480	intergenic_region ; MODIFIER	silent_mutation	Average:45.105; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N
vg0224543759	C -> DEL	N	N	silent_mutation	Average:45.105; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224543759	1.03E-06	NA	mr1276_2	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
vg0224543759	4.76E-06	4.76E-06	mr1276_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