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Detailed information for vg0205952833:

Variant ID: vg0205952833 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5952833
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTCCATCCCAAAATATTTGATGCCGTTGATTTTTTAAAAAATATTTGACCGTTCGTCTTATTAAAATAAACTTAAGTAATTATTAATTCTTTTCCTAT[C/T]
ATTTAATTTATTATTAAATATACTTTTATGTATACATATAGTTTTACACATTTCACAAAAGTTTTTGAATAAGACGAACGGTCAAACATGTTTAAAAAAA

Reverse complement sequence

TTTTTTTAAACATGTTTGACCGTTCGTCTTATTCAAAAACTTTTGTGAAATGTGTAAAACTATATGTATACATAAAAGTATATTTAATAATAAATTAAAT[G/A]
ATAGGAAAAGAATTAATAATTACTTAAGTTTATTTTAATAAGACGAACGGTCAAATATTTTTTAAAAAATCAACGGCATCAAATATTTTGGGATGGAGGG

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	73.70%	26.20%	0.19%	0.00%	NA
All Indica	2759	58.60%	41.30%	0.11%	0.00%	NA
All Japonica	1512	95.60%	4.00%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	70.10%	29.60%	0.34%	0.00%	NA
Indica II	465	62.60%	37.40%	0.00%	0.00%	NA
Indica III	913	50.60%	49.30%	0.11%	0.00%	NA
Indica Intermediate	786	56.70%	43.30%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.70%	0.13%	0.00%	NA
Tropical Japonica	504	91.50%	7.90%	0.60%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0205952833	C -> T	LOC_Os02g11100.1	downstream_gene_variant ; 134.0bp to feature; MODIFIER	silent_mutation	Average:57.169; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0205952833	C -> T	LOC_Os02g11110.1	downstream_gene_variant ; 2167.0bp to feature; MODIFIER	silent_mutation	Average:57.169; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0205952833	C -> T	LOC_Os02g11110.2	downstream_gene_variant ; 2597.0bp to feature; MODIFIER	silent_mutation	Average:57.169; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg0205952833	C -> T	LOC_Os02g11100-LOC_Os02g11110	intergenic_region ; MODIFIER	silent_mutation	Average:57.169; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205952833	NA	7.40E-14	mr1170	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
vg0205952833	NA	9.90E-08	mr1170	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
vg0205952833	3.64E-06	1.19E-11	mr1170_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
vg0205952833	NA	3.50E-09	mr1170_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