Search for Variation information by Variation ID:

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

Detailed information for vg0714480578:

Variant ID: vg0714480578 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14480578
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAAGTGTGGCGTATGTACAAAGTACAATGGAGTAATCACACCAAGGATGAAGCCACTTGGGAGAGCGAAGAATTCTTGAGGATGGAATACCCGCATCT[A/G]
TTCGAAAACAGGTAAGAAAATCTCGGGACGAGATTTATTTAAGGGGGGTAGGTTTGTAACACCCTGAAAATTCGACCAATAAAAAAAATCCAAGCGCCAA

Reverse complement sequence

TTGGCGCTTGGATTTTTTTTATTGGTCGAATTTTCAGGGTGTTACAAACCTACCCCCCTTAAATAAATCTCGTCCCGAGATTTTCTTACCTGTTTTCGAA[T/C]
AGATGCGGGTATTCCATCCTCAAGAATTCTTCGCTCTCCCAAGTGGCTTCATCCTTGGTGTGATTACTCCATTGTACTTTGTACATACGCCACACTTTGC

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	28.10%	0.10%	1.06%	70.72%	NA
All Indica	2759	4.90%	0.20%	1.56%	93.40%	NA
All Japonica	1512	69.40%	0.00%	0.26%	30.36%	NA
Aus	269	8.90%	0.00%	0.37%	90.71%	NA
Indica I	595	6.60%	0.30%	0.67%	92.44%	NA
Indica II	465	5.40%	0.20%	0.86%	93.55%	NA
Indica III	913	3.00%	0.00%	1.64%	95.40%	NA
Indica Intermediate	786	5.50%	0.30%	2.54%	91.73%	NA
Temperate Japonica	767	63.10%	0.00%	0.39%	36.51%	NA
Tropical Japonica	504	93.50%	0.00%	0.20%	6.35%	NA
Japonica Intermediate	241	39.00%	0.00%	0.00%	61.00%	NA
VI/Aromatic	96	82.30%	0.00%	2.08%	15.62%	NA
Intermediate	90	47.80%	0.00%	0.00%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714480578	A -> DEL	LOC_Os07g25340.1	N	frameshift_variant	Average:10.019; most accessible tissue: Callus, score: 31.603	N	N	N	N
vg0714480578	A -> G	LOC_Os07g25340.1	synonymous_variant ; p.Leu1369Leu; LOW	synonymous_codon	Average:10.019; most accessible tissue: Callus, score: 31.603	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714480578	NA	1.25E-06	mr1062	Ind_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
vg0714480578	NA	8.58E-06	mr1386	Ind_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
vg0714480578	NA	1.28E-15	mr1830	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
vg0714480578	NA	2.63E-09	mr1830	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
vg0714480578	NA	1.06E-14	mr1846	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
vg0714480578	NA	1.37E-09	mr1846	Ind_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
vg0714480578	NA	2.66E-06	mr1317_2	Ind_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
vg0714480578	NA	8.77E-06	mr1818_2	Ind_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
vg0714480578	NA	2.09E-12	mr1830_2	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
vg0714480578	NA	3.80E-09	mr1830_2	Ind_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
vg0714480578	NA	5.67E-20	mr1846_2	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
vg0714480578	NA	4.44E-15	mr1846_2	Ind_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