Search for Variation information by Variation ID:

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

Detailed information for vg0314931433:

Variant ID: vg0314931433 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14931433
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGACAGCCATGTTTAGAAGGGCAATTTAATTTGATGATCTAGGGTGTCAAGCGTGTTGAGTATTTTAGATCTTTCAGTTGAGGCATTGAGCCATTGAA[T/C]
ATCTCGGGCATCATGTCCGTCGGTTTGTCCTCGATCTGGCGGTTGTGACACATGTGTAGTTTATGTTACAGTTAAAAAGAAAAGCCTTACGAGCCTATAG

Reverse complement sequence

CTATAGGCTCGTAAGGCTTTTCTTTTTAACTGTAACATAAACTACACATGTGTCACAACCGCCAGATCGAGGACAAACCGACGGACATGATGCCCGAGAT[A/G]
TTCAATGGCTCAATGCCTCAACTGAAAGATCTAAAATACTCAACACGCTTGACACCCTAGATCATCAAATTAAATTGCCCTTCTAAACATGGCTGTCCGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.50%	24.30%	0.13%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	31.50%	68.10%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	97.60%	2.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	9.90%	89.40%	0.65%	0.00%	NA
Tropical Japonica	504	64.90%	35.10%	0.00%	0.00%	NA
Japonica Intermediate	241	30.70%	69.30%	0.00%	0.00%	NA
VI/Aromatic	96	40.60%	59.40%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	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
vg0314931433	T -> C	LOC_Os03g26044.1	upstream_gene_variant ; 1037.0bp to feature; MODIFIER	silent_mutation	Average:65.995; most accessible tissue: Callus, score: 92.514	N	N	N	N
vg0314931433	T -> C	LOC_Os03g26060.1	upstream_gene_variant ; 2441.0bp to feature; MODIFIER	silent_mutation	Average:65.995; most accessible tissue: Callus, score: 92.514	N	N	N	N
vg0314931433	T -> C	LOC_Os03g26044-LOC_Os03g26060	intergenic_region ; MODIFIER	silent_mutation	Average:65.995; most accessible tissue: Callus, score: 92.514	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314931433	NA	7.49E-06	mr1502	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
vg0314931433	NA	3.67E-13	mr1740	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
vg0314931433	4.29E-06	NA	mr1035_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
vg0314931433	4.36E-06	2.80E-07	mr1035_2	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
vg0314931433	NA	1.64E-07	mr1422_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
vg0314931433	8.91E-06	1.05E-38	mr1533_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
vg0314931433	NA	8.12E-14	mr1533_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
vg0314931433	NA	9.50E-06	mr1583_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
vg0314931433	NA	5.11E-06	mr1631_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