Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0426557459:

Variant ID: vg0426557459 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 26557459
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: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTCTCTTCTCACACCATATTGCAACCGCCTAAGTTCGAACCAAGCTCCCGCCTCTAGCTGGATAGATGGCGTGCAGGGTGCAGTAGTGAGGGTGAAGA[C/T]
TGGAGAGGTAGAAGCTTATCGAGACATGGAGATGGAAATGTGGACGGTGGAGAGCGTCATGCGTTTGCTGTTGCCGCCGCCCACAGCTTCGCCACGCCTG

Reverse complement sequence

CAGGCGTGGCGAAGCTGTGGGCGGCGGCAACAGCAAACGCATGACGCTCTCCACCGTCCACATTTCCATCTCCATGTCTCGATAAGCTTCTACCTCTCCA[G/A]
TCTTCACCCTCACTACTGCACCCTGCACGCCATCTATCCAGCTAGAGGCGGGAGCTTGGTTCGAACTTAGGCGGTTGCAATATGGTGTGAGAAGAGACTC

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	75.50%	22.70%	1.74%	0.00%	NA
All Indica	2759	59.10%	38.30%	2.57%	0.00%	NA
All Japonica	1512	99.30%	0.30%	0.40%	0.00%	NA
Aus	269	98.10%	1.50%	0.37%	0.00%	NA
Indica I	595	28.70%	64.00%	7.23%	0.00%	NA
Indica II	465	90.50%	9.00%	0.43%	0.00%	NA
Indica III	913	59.40%	40.30%	0.33%	0.00%	NA
Indica Intermediate	786	63.20%	33.80%	2.93%	0.00%	NA
Temperate Japonica	767	99.50%	0.10%	0.39%	0.00%	NA
Tropical Japonica	504	98.80%	0.60%	0.60%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg0426557459	C -> T	LOC_Os04g44870.1	upstream_gene_variant ; 1351.0bp to feature; MODIFIER	silent_mutation	Average:74.423; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0426557459	C -> T	LOC_Os04g44850.1	downstream_gene_variant ; 2568.0bp to feature; MODIFIER	silent_mutation	Average:74.423; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N
vg0426557459	C -> T	LOC_Os04g44850-LOC_Os04g44870	intergenic_region ; MODIFIER	silent_mutation	Average:74.423; most accessible tissue: Minghui63 panicle, score: 83.421	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0426557459	1.94E-06	NA	mr1873_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
vg0426557459	NA	5.85E-06	mr1873_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