Search for Variation information by Variation ID:

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

Detailed information for vg0400672500:

Variant ID: vg0400672500 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 672500
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCAACTTACAACAAAAAGGTTCGACCGACGGAGCTGTTGCCTGGTCATCTTGTCCTAAGAAAGAAGGTGAACCCGATAGCCGTTGGCAAGCTTGAATC[G/A]
AAGTGGGAAGGACCGTACCTCATCAAGCACAAGTCCAAGACGGGGTCCTTTCGACTGGCGACACTGGAAGGCGAAGAGTTCGACCATTCCTGGAACGCTG

Reverse complement sequence

CAGCGTTCCAGGAATGGTCGAACTCTTCGCCTTCCAGTGTCGCCAGTCGAAAGGACCCCGTCTTGGACTTGTGCTTGATGAGGTACGGTCCTTCCCACTT[C/T]
GATTCAAGCTTGCCAACGGCTATCGGGTTCACCTTCTTTCTTAGGACAAGATGACCAGGCAACAGCTCCGTCGGTCGAACCTTTTTGTTGTAAGTTGCCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.40%	3.40%	3.24%	0.00%	NA
All Indica	2759	88.90%	5.60%	5.47%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	87.40%	1.00%	11.60%	0.00%	NA
Indica II	465	75.10%	16.30%	8.60%	0.00%	NA
Indica III	913	98.80%	1.00%	0.22%	0.00%	NA
Indica Intermediate	786	86.90%	8.00%	5.09%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	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
vg0400672500	G -> A	LOC_Os04g02080.1	synonymous_variant ; p.Ser443Ser; LOW	synonymous_codon	Average:49.124; most accessible tissue: Zhenshan97 flag leaf, score: 70.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400672500	NA	6.62E-06	mr1120	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
vg0400672500	NA	2.71E-09	mr1565	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
vg0400672500	NA	5.42E-08	mr1715	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
vg0400672500	NA	9.57E-08	mr1771	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