Search for Variation information by Variation ID:

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

Detailed information for vg0432167290:

Variant ID: vg0432167290 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 32167290
Reference Allele: CA	Alternative Allele: TA,C
Primary Allele: CA	Secondary Allele: TA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGCATCCCCGACCCGGCCGCCGTCGCCGCCGTGCCGCAGCCGGGGCTCGCCGGCTTCACCGACTGGACCCAGCCTTTCATGTGAGTTATATATACAAGC[CA/TA,C]
ATTAATTAACTCGTACTAGCTACCATATCATATGGAGAGCTAGCTTAGCTGAGATCGATCCTGACATGTTTGCATGCGATTTTGTGTACGTTTCATCAGG

Reverse complement sequence

CCTGATGAAACGTACACAAAATCGCATGCAAACATGTCAGGATCGATCTCAGCTAAGCTAGCTCTCCATATGATATGGTAGCTAGTACGAGTTAATTAAT[TG/TA,G]
GCTTGTATATATAACTCACATGAAAGGCTGGGTCCAGTCGGTGAAGCCGGCGAGCCCCGGCTGCGGCACGGCGGCGACGGCGGCCGGGTCGGGGATGCTC

Allele Frequencies:

Populations	Population Size	Frequency of CA(primary allele)	Frequency of TA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.70%	8.30%	0.04%	0.00%	C: 0.04%
All Indica	2759	98.60%	1.30%	0.04%	0.00%	C: 0.07%
All Japonica	1512	88.60%	11.40%	0.07%	0.00%	NA
Aus	269	37.90%	62.10%	0.00%	0.00%	NA
Indica I	595	96.80%	3.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.20%	0.50%	0.00%	0.00%	C: 0.22%
Indica Intermediate	786	98.30%	1.50%	0.13%	0.00%	NA
Temperate Japonica	767	94.10%	5.90%	0.00%	0.00%	NA
Tropical Japonica	504	77.60%	22.40%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	5.80%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg0432167290	CA -> C	LOC_Os04g53980.1	upstream_gene_variant ; 1617.0bp to feature; MODIFIER	silent_mutation	Average:77.36; most accessible tissue: Callus, score: 88.108	N	N	N	N
vg0432167290	CA -> C	LOC_Os04g53990.1	intron_variant ; MODIFIER	silent_mutation	Average:77.36; most accessible tissue: Callus, score: 88.108	N	N	N	N
vg0432167290	CA -> TA	LOC_Os04g53980.1	upstream_gene_variant ; 1616.0bp to feature; MODIFIER	silent_mutation	Average:77.36; most accessible tissue: Callus, score: 88.108	N	N	N	N
vg0432167290	CA -> TA	LOC_Os04g53990.1	intron_variant ; MODIFIER	silent_mutation	Average:77.36; most accessible tissue: Callus, score: 88.108	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432167290	NA	9.78E-07	mr1057	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
vg0432167290	NA	2.72E-07	mr1073	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
vg0432167290	NA	9.12E-06	mr1153	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
vg0432167290	NA	6.19E-07	mr1184	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
vg0432167290	NA	2.31E-06	mr1331	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
vg0432167290	NA	1.96E-06	mr1345	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
vg0432167290	NA	4.13E-06	mr1353	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
vg0432167290	NA	1.84E-06	mr1365	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
vg0432167290	2.91E-08	NA	mr1550	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
vg0432167290	2.06E-07	NA	mr1550	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