Search for Variation information by Variation ID:

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

Detailed information for vg0321793624:

Variant ID: vg0321793624 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21793624
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGGCGGAGATTGCGGAATCACAAGCGTTCTCTGCGGTCTTGTTAGCCGATGCCAACCGAGCAGCAAGTCCCGTCGTCGTCGTGCATAAGAGGCCGAC[A/G]
CCGGAGACGGAGAAGGAGCAGGATCAGGAGCCGCCACGACAGAGGCGCCGCACAGGAGACAGTGCCGCACAAGACTAGCGAGCTCATGTCGATCGCCACT

Reverse complement sequence

AGTGGCGATCGACATGAGCTCGCTAGTCTTGTGCGGCACTGTCTCCTGTGCGGCGCCTCTGTCGTGGCGGCTCCTGATCCTGCTCCTTCTCCGTCTCCGG[T/C]
GTCGGCCTCTTATGCACGACGACGACGGGACTTGCTGCTCGGTTGGCATCGGCTAACAAGACCGCAGAGAACGCTTGTGATTCCGCAATCTCCGCCTCGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.90%	31.00%	0.11%	0.00%	NA
All Indica	2759	97.30%	2.60%	0.14%	0.00%	NA
All Japonica	1512	10.30%	89.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.50%	3.50%	0.00%	0.00%	NA
Indica II	465	97.00%	2.60%	0.43%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	4.10%	0.25%	0.00%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	10.10%	89.90%	0.00%	0.00%	NA
Japonica Intermediate	241	35.70%	64.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	58.90%	40.00%	1.11%	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
vg0321793624	A -> G	LOC_Os03g39240.1	synonymous_variant ; p.Thr255Thr; LOW	synonymous_codon	Average:38.704; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321793624	NA	1.42E-22	mr1548	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
vg0321793624	NA	2.93E-21	mr1689	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
vg0321793624	NA	1.27E-07	mr1718	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
vg0321793624	4.95E-08	3.80E-115	mr1750	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
vg0321793624	NA	4.72E-11	mr1750	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
vg0321793624	4.59E-06	4.59E-06	mr1750	Jap_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
vg0321793624	NA	3.86E-37	mr1828	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
vg0321793624	NA	1.38E-14	mr1874	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
vg0321793624	NA	1.35E-33	mr1932	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
vg0321793624	7.67E-06	7.67E-06	mr1312_2	Jap_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
vg0321793624	NA	4.88E-19	mr1750_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
vg0321793624	NA	1.17E-07	mr1987_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