Search for Variation information by Variation ID:

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

Detailed information for vg0107845967:

Variant ID: vg0107845967 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7845967
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

TGATTCACGATCAGAATTAAGCAGAGACTCTCTCAAAAAAAAAGAGAAGCAGATCGACTGTAAAATGTAGCAAATTCTCCATATATGGGAGTACTCCATC[A/C]
ATTTCAAAATAGATCAACCTAGATTAAAATAGAATAGTACAACGAATCTTGACGGTTCCTTTTCAACATAGAATTATTTTGGAACGGATCGGAAGGAGTA

Reverse complement sequence

TACTCCTTCCGATCCGTTCCAAAATAATTCTATGTTGAAAAGGAACCGTCAAGATTCGTTGTACTATTCTATTTTAATCTAGGTTGATCTATTTTGAAAT[T/G]
GATGGAGTACTCCCATATATGGAGAATTTGCTACATTTTACAGTCGATCTGCTTCTCTTTTTTTTTGAGAGAGTCTCTGCTTAATTCTGATCGTGAATCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.70%	42.80%	0.13%	0.36%	NA
All Indica	2759	84.80%	14.50%	0.18%	0.51%	NA
All Japonica	1512	3.60%	96.40%	0.00%	0.00%	NA
Aus	269	87.40%	12.60%	0.00%	0.00%	NA
Indica I	595	83.20%	16.30%	0.17%	0.34%	NA
Indica II	465	93.80%	5.80%	0.22%	0.22%	NA
Indica III	913	88.80%	10.20%	0.33%	0.66%	NA
Indica Intermediate	786	76.10%	23.30%	0.00%	0.64%	NA
Temperate Japonica	767	6.10%	93.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	50.00%	45.60%	1.11%	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
vg0107845967	A -> DEL	N	N	silent_mutation	Average:58.345; most accessible tissue: Callus, score: 93.14	N	N	N	N
vg0107845967	A -> C	LOC_Os01g14010.1	upstream_gene_variant ; 1775.0bp to feature; MODIFIER	silent_mutation	Average:58.345; most accessible tissue: Callus, score: 93.14	N	N	N	N
vg0107845967	A -> C	LOC_Os01g14000.1	downstream_gene_variant ; 1309.0bp to feature; MODIFIER	silent_mutation	Average:58.345; most accessible tissue: Callus, score: 93.14	N	N	N	N
vg0107845967	A -> C	LOC_Os01g14000-LOC_Os01g14010	intergenic_region ; MODIFIER	silent_mutation	Average:58.345; most accessible tissue: Callus, score: 93.14	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107845967	5.41E-07	5.41E-07	mr1770	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
vg0107845967	NA	5.39E-06	mr1329_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
vg0107845967	NA	2.55E-06	mr1982_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