Search for Variation information by Variation ID:

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

Detailed information for vg0211327689:

Variant ID: vg0211327689 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11327689
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCATGTCCTTGCGACTGATGGGCCCGCACGGGCCCCGCGCAAGGGAAAGACCACCGGCGACAAGCCGAGCTCCACTGCTCCATCCGGCGAGGGCCGGTC[G/A]
GCAGACAAGTGGTACTCGGTGCACAACACTTATCGGCACAGTCTCGCTGACTGCCGCTCGGTCAAGAATTTGGCCGAGCGGTTCCGGAAAGCCGATGAGG

Reverse complement sequence

CCTCATCGGCTTTCCGGAACCGCTCGGCCAAATTCTTGACCGAGCGGCAGTCAGCGAGACTGTGCCGATAAGTGTTGTGCACCGAGTACCACTTGTCTGC[C/T]
GACCGGCCCTCGCCGGATGGAGCAGTGGAGCTCGGCTTGTCGCCGGTGGTCTTTCCCTTGCGCGGGGCCCGTGCGGGCCCATCAGTCGCAAGGACATGGC

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	65.30%	2.80%	8.00%	23.87%	NA
All Indica	2759	43.00%	4.80%	13.34%	38.85%	NA
All Japonica	1512	98.80%	0.00%	0.13%	1.06%	NA
Aus	269	93.70%	0.00%	1.86%	4.46%	NA
Indica I	595	25.00%	8.20%	8.40%	58.32%	NA
Indica II	465	43.40%	1.10%	12.47%	43.01%	NA
Indica III	913	53.80%	5.70%	17.63%	22.89%	NA
Indica Intermediate	786	43.90%	3.30%	12.60%	40.20%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	98.00%	0.00%	0.40%	1.59%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	67.80%	1.10%	1.11%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0211327689	G -> A	LOC_Os02g19390.1	synonymous_variant ; p.Ser171Ser; LOW	synonymous_codon	Average:19.581; most accessible tissue: Callus, score: 49.162	N	N	N	N
vg0211327689	G -> DEL	LOC_Os02g19390.1	N	frameshift_variant	Average:19.581; most accessible tissue: Callus, score: 49.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211327689	2.39E-06	2.62E-06	mr1732	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