Search for Variation information by Variation ID:

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

Detailed information for vg1213321086:

Variant ID: vg1213321086 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13321086
Reference Allele: C	Alternative Allele: T,A
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: 43. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATTCGATGGCCTTGAGCTACCCCACGTTCTTCAACATAATAATGAGGCAGCCGACCGGCTGGCTAATTTTGGTTCAAAACGAGAAGCAGCTCCTTC[C/T,A]
GACGTGTTCGTTGAACATCTTTATGAGCCAACCGTACCAAGGAAAGAAATAATCGAGGCCACGGACACTCAAGAAGTAAGCATGATTGAAGCCGACTGGA

Reverse complement sequence

TCCAGTCGGCTTCAATCATGCTTACTTCTTGAGTGTCCGTGGCCTCGATTATTTCTTTCCTTGGTACGGTTGGCTCATAAAGATGTTCAACGAACACGTC[G/A,T]
GAAGGAGCTGCTTCTCGTTTTGAACCAAAATTAGCCAGCCGGTCGGCTGCCTCATTATTATGTTGAAGAACGTGGGGTAGCTCAAGGCCATCGAATTTAT

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	52.00%	13.00%	24.97%	9.84%	A: 0.21%
All Indica	2759	46.40%	17.30%	31.68%	4.64%	NA
All Japonica	1512	55.40%	7.90%	15.28%	21.36%	NA
Aus	269	83.30%	0.40%	13.38%	2.97%	NA
Indica I	595	50.10%	10.40%	37.98%	1.51%	NA
Indica II	465	40.20%	11.40%	38.06%	10.32%	NA
Indica III	913	44.60%	24.80%	26.73%	3.94%	NA
Indica Intermediate	786	49.50%	17.20%	28.88%	4.45%	NA
Temperate Japonica	767	83.40%	0.40%	4.04%	12.13%	NA
Tropical Japonica	504	20.60%	18.50%	28.97%	31.94%	NA
Japonica Intermediate	241	39.00%	10.00%	22.41%	28.63%	NA
VI/Aromatic	96	59.40%	3.10%	23.96%	3.12%	A: 10.42%
Intermediate	90	62.20%	16.70%	17.78%	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
vg1213321086	C -> DEL	LOC_Os12g23530.1	N	frameshift_variant	Average:6.851; most accessible tissue: Callus, score: 12.164	N	N	N	N
vg1213321086	C -> A	LOC_Os12g23530.1	synonymous_variant ; p.Ser411Ser; LOW	synonymous_codon	Average:6.851; most accessible tissue: Callus, score: 12.164	N	N	N	N
vg1213321086	C -> T	LOC_Os12g23530.1	synonymous_variant ; p.Ser411Ser; LOW	synonymous_codon	Average:6.851; most accessible tissue: Callus, score: 12.164	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213321086	3.51E-06	3.51E-06	mr1929	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