Search for Variation information by Variation ID:

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

Detailed information for vg1218248661:

Variant ID: vg1218248661 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18248661
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAAATCACATGCGAGCCACACACACACAAGCAAACTTAAAACAAGCAAACTAACACATCGATCTAAGACAACGACTTAACAAGTCACTCTAGTTCTTC[C/T]
AAGCATCGGAGGTCGATTGAGGGCTCGTCTTCATCATCTTGAGTTGCTACCCACTCAATCTTGGAATTGATGCGCTTGGATTCTTCTTCTTCATCACTAC

Reverse complement sequence

GTAGTGATGAAGAAGAAGAATCCAAGCGCATCAATTCCAAGATTGAGTGGGTAGCAACTCAAGATGATGAAGACGAGCCCTCAATCGACCTCCGATGCTT[G/A]
GAAGAACTAGAGTGACTTGTTAAGTCGTTGTCTTAGATCGATGTGTTAGTTTGCTTGTTTTAAGTTTGCTTGTGTGTGTGTGGCTCGCATGTGATTTACA

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	17.30%	10.50%	19.11%	53.13%	NA
All Indica	2759	1.40%	6.70%	13.63%	78.25%	NA
All Japonica	1512	48.90%	16.50%	29.03%	5.56%	NA
Aus	269	0.00%	3.70%	10.41%	85.87%	NA
Indica I	595	1.20%	1.00%	3.53%	94.29%	NA
Indica II	465	2.20%	9.70%	15.91%	72.26%	NA
Indica III	913	0.40%	9.70%	18.51%	71.30%	NA
Indica Intermediate	786	2.40%	5.60%	14.25%	77.74%	NA
Temperate Japonica	767	67.40%	3.70%	21.38%	7.56%	NA
Tropical Japonica	504	31.70%	22.40%	42.86%	2.98%	NA
Japonica Intermediate	241	26.10%	44.80%	24.48%	4.56%	NA
VI/Aromatic	96	11.50%	34.40%	43.75%	10.42%	NA
Intermediate	90	30.00%	20.00%	20.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218248661	C -> DEL	LOC_Os12g30410.1	N	frameshift_variant	Average:5.934; most accessible tissue: Callus, score: 17.632	N	N	N	N
vg1218248661	C -> T	LOC_Os12g30410.1	synonymous_variant ; p.Leu323Leu; LOW	synonymous_codon	Average:5.934; most accessible tissue: Callus, score: 17.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218248661	NA	6.54E-07	mr1338	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
vg1218248661	2.57E-06	NA	mr1563	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
vg1218248661	NA	3.35E-09	mr1563	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