Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0803968574:

Variant ID: vg0803968574 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3968574
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, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAGGAAAATAAATCTAGGGTTAAGTTAAAATTCGTGGAGGTGGAGGGGGCCTAGTCTATTACAAGGCTCAAGGCCCAAGTTCGGTTTTAGCAACAACA[C/T]
TGTCTTGTTTTGGCGATTCCCGTTGACTCGAGATGAATTTGGACATGGTACCAGATGCGTTTGAAAGGTGGCGAGATAAGCTTTCCACGAAGTCCAAGAT

Reverse complement sequence

ATCTTGGACTTCGTGGAAAGCTTATCTCGCCACCTTTCAAACGCATCTGGTACCATGTCCAAATTCATCTCGAGTCAACGGGAATCGCCAAAACAAGACA[G/A]
TGTTGTTGCTAAAACCGAACTTGGGCCTTGAGCCTTGTAATAGACTAGGCCCCCTCCACCTCCACGAATTTTAACTTAACCCTAGATTTATTTTCCTCTA

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	97.20%	2.30%	0.51%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	91.50%	6.90%	1.59%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.80%	10.20%	3.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	10.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0803968574	C -> T	LOC_Os08g07100.1	upstream_gene_variant ; 3642.0bp to feature; MODIFIER	silent_mutation	Average:39.319; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0803968574	C -> T	LOC_Os08g07080.1	downstream_gene_variant ; 2908.0bp to feature; MODIFIER	silent_mutation	Average:39.319; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg0803968574	C -> T	LOC_Os08g07090.1	intron_variant ; MODIFIER	silent_mutation	Average:39.319; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803968574	4.66E-06	4.66E-06	mr1973	Jap_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
vg0803968574	5.69E-06	1.03E-09	mr1062_2	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