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Detailed information for vg0526341867:

Variant ID: vg0526341867 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 26341867
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.29, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCGCCGGCCAGGCAATTGTATCGTTTACGTCGGCGTTGTTCAAGGCTGCATCAGTACATTCGACCTCTTGCATTGCTCTAGTTTGGATGATATATTTG[C/T]
CTACCTATTTATCATATGTCTCTGTTAATCTAGTTTTAGCATATCAATTTAGCTCTATCGGCTGCTTCTCGTTTTAGGGTTTCTGCCGGTATCGGCTAAA

Reverse complement sequence

TTTAGCCGATACCGGCAGAAACCCTAAAACGAGAAGCAGCCGATAGAGCTAAATTGATATGCTAAAACTAGATTAACAGAGACATATGATAAATAGGTAG[G/A]
CAAATATATCATCCAAACTAGAGCAATGCAAGAGGTCGAATGTACTGATGCAGCCTTGAACAACGCCGACGTAAACGATACAATTGCCTGGCCGGCGGAA

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	61.60%	38.00%	0.02%	0.42%	NA
All Indica	2759	91.50%	8.00%	0.00%	0.51%	NA
All Japonica	1512	0.90%	98.90%	0.00%	0.26%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.00%	0.50%	NA
Indica II	465	68.20%	30.50%	0.00%	1.29%	NA
Indica III	913	97.00%	3.00%	0.00%	0.00%	NA
Indica Intermediate	786	92.70%	6.60%	0.00%	0.64%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.00%	0.00%	0.40%	NA
Japonica Intermediate	241	0.40%	98.80%	0.00%	0.83%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	41.10%	55.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0526341867	C -> T	LOC_Os05g45400.1	upstream_gene_variant ; 4543.0bp to feature; MODIFIER	silent_mutation	Average:45.872; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0526341867	C -> T	LOC_Os05g45410.1	upstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:45.872; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0526341867	C -> T	LOC_Os05g45400-LOC_Os05g45410	intergenic_region ; MODIFIER	silent_mutation	Average:45.872; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N
vg0526341867	C -> DEL	N	N	silent_mutation	Average:45.872; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0526341867	NA	2.85E-10	mr1232	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
vg0526341867	2.02E-06	NA	mr1977	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
vg0526341867	NA	4.03E-06	mr1344_2	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