Search for Variation information by Variation ID:

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

Detailed information for vg0119898300:

Variant ID: vg0119898300 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19898300
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCACTCACATTTTGCTCTGACTCTATCACCCTCATCCTTTACAAACTTCACATACCTTCTGTTGGCTAGTGCATGTTTTATAACTGCATCCTTGAACT[C/G]
TTTCTTACAATCAAATAGCTGGCCTAGAGTAAAAGTCGGAGTGCTGCTACTACTACCTCTGAACCTTGGATACTTACTCCTTTTAGTGATCAACTGACCA

Reverse complement sequence

TGGTCAGTTGATCACTAAAAGGAGTAAGTATCCAAGGTTCAGAGGTAGTAGTAGCAGCACTCCGACTTTTACTCTAGGCCAGCTATTTGATTGTAAGAAA[G/C]
AGTTCAAGGATGCAGTTATAAAACATGCACTAGCCAACAGAAGGTATGTGAAGTTTGTAAAGGATGAGGGTGATAGAGTCAGAGCAAAATGTGAGTGGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.90%	2.50%	3.62%	8.99%	NA
All Indica	2759	75.80%	4.10%	6.05%	14.10%	NA
All Japonica	1512	99.30%	0.00%	0.00%	0.66%	NA
Aus	269	90.70%	0.00%	0.74%	8.55%	NA
Indica I	595	71.30%	11.80%	13.61%	3.36%	NA
Indica II	465	79.80%	1.90%	1.94%	16.34%	NA
Indica III	913	70.50%	0.30%	5.37%	23.77%	NA
Indica Intermediate	786	83.00%	3.80%	3.56%	9.67%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	4.40%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119898300	C -> G	LOC_Os01g35960.1	missense_variant ; p.Glu319Gln; MODERATE	nonsynonymous_codon ; E319Q	Average:30.392; most accessible tissue: Minghui63 young leaf, score: 55.178	unknown	unknown	TOLERATED	0.64
vg0119898300	C -> DEL	LOC_Os01g35960.1	N	frameshift_variant	Average:30.392; most accessible tissue: Minghui63 young leaf, score: 55.178	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119898300	NA	6.01E-06	mr1038	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
vg0119898300	NA	1.76E-06	mr1038	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
vg0119898300	NA	9.21E-06	mr1219	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
vg0119898300	NA	4.01E-07	mr1389	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
vg0119898300	NA	1.18E-06	mr1389	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
vg0119898300	4.12E-06	4.12E-06	mr1849	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
vg0119898300	NA	7.30E-07	mr1038_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