Search for Variation information by Variation ID:

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

Detailed information for vg1221401988:

Variant ID: vg1221401988 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21401988
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGCTGGCCTTGGAACTCTTCAAACTCTTCTTCCGCGAAAACGGACTCTCCGGTAACGACGGAATCTAAGCAGAAAAGAGCAAAATCACCAAAACAGCAC[T/A]
TAAACAAACATGAACAGTACATGTGGATATTTTTAATGTGTAGATCTCAATTTTAGAAAAATTTAGAGACTTGAACCAACTAAATCGGAGCTAAGATGAA

Reverse complement sequence

TTCATCTTAGCTCCGATTTAGTTGGTTCAAGTCTCTAAATTTTTCTAAAATTGAGATCTACACATTAAAAATATCCACATGTACTGTTCATGTTTGTTTA[A/T]
GTGCTGTTTTGGTGATTTTGCTCTTTTCTGCTTAGATTCCGTCGTTACCGGAGAGTCCGTTTTCGCGGAAGAAGAGTTTGAAGAGTTCCAAGGCCAGCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	0.30%	14.90%	22.73%	NA
All Indica	2759	54.30%	0.00%	19.97%	25.70%	NA
All Japonica	1512	84.80%	0.70%	6.55%	8.00%	NA
Aus	269	14.90%	0.00%	10.41%	74.72%	NA
Indica I	595	57.10%	0.00%	6.89%	35.97%	NA
Indica II	465	70.10%	0.00%	10.75%	19.14%	NA
Indica III	913	39.40%	0.00%	35.60%	24.97%	NA
Indica Intermediate	786	60.10%	0.10%	17.18%	22.65%	NA
Temperate Japonica	767	88.00%	0.40%	2.87%	8.74%	NA
Tropical Japonica	504	79.80%	1.20%	12.10%	6.94%	NA
Japonica Intermediate	241	85.10%	0.40%	6.64%	7.88%	NA
VI/Aromatic	96	57.30%	0.00%	14.58%	28.12%	NA
Intermediate	90	67.80%	1.10%	13.33%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221401988	T -> DEL	N	N	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg1221401988	T -> A	LOC_Os12g35180.1	upstream_gene_variant ; 4605.0bp to feature; MODIFIER	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg1221401988	T -> A	LOC_Os12g35239.1	upstream_gene_variant ; 3839.0bp to feature; MODIFIER	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg1221401988	T -> A	LOC_Os12g35190.1	downstream_gene_variant ; 1672.0bp to feature; MODIFIER	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg1221401988	T -> A	LOC_Os12g35200.1	downstream_gene_variant ; 1483.0bp to feature; MODIFIER	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N
vg1221401988	T -> A	LOC_Os12g35190-LOC_Os12g35200	intergenic_region ; MODIFIER	silent_mutation	Average:39.763; most accessible tissue: Zhenshan97 flag leaf, score: 61.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221401988	1.01E-06	3.47E-06	mr1895	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