Search for Variation information by Variation ID:

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

Detailed information for vg1218179477:

Variant ID: vg1218179477 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18179477
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAGCATGGTCTTGATAAGACGCAAAAGATCTTGCTGGCAGACATTCTAAGATGTCTGGCCTGTATGTCACAAAGTCTCGTGAAGTCTAGAAAAGTTGT[C/T]
GAGGATGAAGCTCCACATGAACTCTTACATGCACAAGACCACAGACAATGAGAAATTTTGAGAGAAGTTTCTTTGACCAATCACAAATCTCAAAGTAGTT

Reverse complement sequence

AACTACTTTGAGATTTGTGATTGGTCAAAGAAACTTCTCTCAAAATTTCTCATTGTCTGTGGTCTTGTGCATGTAAGAGTTCATGTGGAGCTTCATCCTC[G/A]
ACAACTTTTCTAGACTTCACGAGACTTTGTGACATACAGGCCAGACATCTTAGAATGTCTGCCAGCAAGATCTTTTGCGTCTTATCAAGACCATGCTTGT

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	77.80%	3.60%	0.74%	17.84%	NA
All Indica	2759	96.50%	1.90%	0.14%	1.49%	NA
All Japonica	1512	44.40%	7.40%	1.59%	46.56%	NA
Aus	269	94.40%	0.00%	0.00%	5.58%	NA
Indica I	595	98.30%	0.00%	0.00%	1.68%	NA
Indica II	465	90.50%	9.00%	0.00%	0.43%	NA
Indica III	913	99.30%	0.00%	0.11%	0.55%	NA
Indica Intermediate	786	95.30%	1.30%	0.38%	3.05%	NA
Temperate Japonica	767	65.60%	0.30%	0.91%	33.25%	NA
Tropical Japonica	504	8.90%	19.60%	3.17%	68.25%	NA
Japonica Intermediate	241	51.50%	4.60%	0.41%	43.57%	NA
VI/Aromatic	96	25.00%	4.20%	3.12%	67.71%	NA
Intermediate	90	74.40%	1.10%	4.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218179477	C -> DEL	N	N	silent_mutation	Average:36.406; most accessible tissue: Callus, score: 73.926	N	N	N	N
vg1218179477	C -> T	LOC_Os12g30290-LOC_Os12g30310	intergenic_region ; MODIFIER	silent_mutation	Average:36.406; most accessible tissue: Callus, score: 73.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218179477	NA	6.37E-07	mr1364	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
vg1218179477	NA	4.08E-07	mr1443	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
vg1218179477	NA	6.20E-06	mr1884	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
vg1218179477	4.10E-06	1.91E-08	mr1498_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
vg1218179477	2.45E-06	2.45E-06	mr1925_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