Search for Variation information by Variation ID:

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

Detailed information for vg0206101334:

Variant ID: vg0206101334 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6101334
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCATGTAGATGAGAAAGAGGTTGGGCTCTTACCACCGAGGAAGCAAACGAATGCGCAATACACGAGCGTCACAGGGCCATGAGAAAAGAATGGGGGAAA[A/G]
GAAATATAAGACTTCAAGCTGTATTAAGCTGATGAATTGAAAAATTGAAAATACTTGAAGGTTGAAAGGACGATTAGTTGAGCCGGGCCGGGCACCATAG

Reverse complement sequence

CTATGGTGCCCGGCCCGGCTCAACTAATCGTCCTTTCAACCTTCAAGTATTTTCAATTTTTCAATTCATCAGCTTAATACAGCTTGAAGTCTTATATTTC[T/C]
TTTCCCCCATTCTTTTCTCATGGCCCTGTGACGCTCGTGTATTGCGCATTCGTTTGCTTCCTCGGTGGTAAGAGCCCAACCTCTTTCTCATCTACATGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.70%	4.50%	7.24%	16.53%	NA
All Indica	2759	56.20%	7.10%	9.17%	27.51%	NA
All Japonica	1512	95.20%	0.00%	4.50%	0.26%	NA
Aus	269	92.60%	6.70%	0.37%	0.37%	NA
Indica I	595	57.60%	5.70%	10.25%	26.39%	NA
Indica II	465	67.50%	0.40%	5.38%	26.67%	NA
Indica III	913	49.90%	9.70%	8.43%	31.87%	NA
Indica Intermediate	786	55.60%	9.20%	11.45%	23.79%	NA
Temperate Japonica	767	91.70%	0.00%	8.08%	0.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	97.90%	0.00%	1.66%	0.41%	NA
VI/Aromatic	96	75.00%	0.00%	17.71%	7.29%	NA
Intermediate	90	85.60%	0.00%	3.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206101334	A -> G	LOC_Os02g11800.1	downstream_gene_variant ; 3329.0bp to feature; MODIFIER	silent_mutation	Average:25.944; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0206101334	A -> G	LOC_Os02g11790-LOC_Os02g11800	intergenic_region ; MODIFIER	silent_mutation	Average:25.944; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N
vg0206101334	A -> DEL	N	N	silent_mutation	Average:25.944; most accessible tissue: Minghui63 root, score: 55.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206101334	2.72E-06	NA	mr1973_2	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