Search for Variation information by Variation ID:

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

Detailed information for vg0220240426:

Variant ID: vg0220240426 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20240426
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGAGGCATTGGATGCTCATACGATAATCACGGGACTACGTAACATGTTTGAGGACCAAGCAAGGGCTGAGAGGTTTAATACCTCAAAGTCCTTGTTTGC[G/A]
TGCAGGCTTGCAGAAGGTAATCCAGTGAGCCCACATGTGATCAAAATAATTGGTTACACCGAGAGTCTGGATAAGCTTGGCTTTCCCCTTAGCCAAGAGT

Reverse complement sequence

ACTCTTGGCTAAGGGGAAAGCCAAGCTTATCCAGACTCTCGGTGTAACCAATTATTTTGATCACATGTGGGCTCACTGGATTACCTTCTGCAAGCCTGCA[C/T]
GCAAACAAGGACTTTGAGGTATTAAACCTCTCAGCCCTTGCTTGGTCCTCAAACATGTTACGTAGTCCCGTGATTATCGTATGAGCATCCAATGCCTCAT

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	89.60%	8.90%	1.44%	0.00%	NA
All Indica	2759	98.70%	0.80%	0.43%	0.00%	NA
All Japonica	1512	82.10%	17.80%	0.07%	0.00%	NA
Aus	269	74.00%	6.30%	19.70%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	99.20%	0.50%	0.22%	0.00%	NA
Indica Intermediate	786	98.00%	1.00%	1.02%	0.00%	NA
Temperate Japonica	767	82.50%	17.50%	0.00%	0.00%	NA
Tropical Japonica	504	79.20%	20.80%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.40%	0.41%	0.00%	NA
VI/Aromatic	96	1.00%	97.90%	1.04%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg0220240426	G -> A	LOC_Os02g33960.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:25.662; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0220240426	G -> A	LOC_Os02g33970.1	upstream_gene_variant ; 1147.0bp to feature; MODIFIER	silent_mutation	Average:25.662; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220240426	NA	3.62E-06	mr1341_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
vg0220240426	NA	6.83E-08	mr1585_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
vg0220240426	3.59E-06	8.37E-07	mr1955_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