Search for Variation information by Variation ID:

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

Detailed information for vg0336159623:

Variant ID: vg0336159623 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 36159623
Reference Allele: TA	Alternative Allele: TAA,AA,TAAA,T
Primary Allele: TA	Secondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGTATGCCATGGTGGCGCGTACGTCAGTAGAACCCATATATCAGTCACATATAGAAAAAATCAAGAACATATTTTTCTCCTCTATTTTTTTATTTTTT[TA/TAA,AA,TAAA,T]
AAAAAAATAAAAAAAATCCCTTTCTCTTCTCTTTATAAATTTTATTTTTTTTTCTATATGGCTGGCATATGGATCCCACTAACACGAGCGTCACTGTGAC

Reverse complement sequence

GTCACAGTGACGCTCGTGTTAGTGGGATCCATATGCCAGCCATATAGAAAAAAAAATAAAATTTATAAAGAGAAGAGAAAGGGATTTTTTTTATTTTTTT[TA/TTA,TT,TTTA,A]
AAAAAATAAAAAAATAGAGGAGAAAAATATGTTCTTGATTTTTTCTATATGTGACTGATATATGGGTTCTACTGACGTACGCGCCACCATGGCATACCAC

Allele Frequencies:

Populations	Population Size	Frequency of TA(primary allele)	Frequency of AA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.50%	17.80%	2.43%	0.00%	TAA: 7.30%; TAAA: 0.02%
All Indica	2759	63.40%	26.90%	0.98%	0.00%	TAA: 8.74%
All Japonica	1512	87.50%	2.50%	3.11%	0.00%	TAA: 6.81%; TAAA: 0.07%
Aus	269	73.60%	13.00%	13.38%	0.00%	NA
Indica I	595	83.00%	12.90%	0.50%	0.00%	TAA: 3.53%
Indica II	465	72.30%	22.20%	0.22%	0.00%	TAA: 5.38%
Indica III	913	46.80%	37.20%	0.77%	0.00%	TAA: 15.22%
Indica Intermediate	786	62.70%	28.10%	2.04%	0.00%	TAA: 7.12%
Temperate Japonica	767	95.30%	0.90%	2.09%	0.00%	TAA: 1.69%
Tropical Japonica	504	75.60%	3.40%	4.17%	0.00%	TAA: 16.67%; TAAA: 0.20%
Japonica Intermediate	241	87.60%	5.80%	4.15%	0.00%	TAA: 2.49%
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	73.30%	20.00%	5.56%	0.00%	TAA: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0336159623	TA -> T	LOC_Os03g63980-LOC_Os03g63990	intergenic_region ; MODIFIER	N	Average:40.788; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0336159623	TA -> TAA	LOC_Os03g63980-LOC_Os03g63990	intergenic_region ; MODIFIER	silent_mutation	Average:40.788; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0336159623	TA -> AA	LOC_Os03g63980-LOC_Os03g63990	intergenic_region ; MODIFIER	silent_mutation	Average:40.788; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0336159623	TA -> TAAA	LOC_Os03g63980-LOC_Os03g63990	intergenic_region ; MODIFIER	N	Average:40.788; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0336159623	2.39E-06	9.16E-06	mr1368	Jap_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
vg0336159623	3.17E-06	3.17E-06	mr1384	Jap_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