Search for Variation information by Variation ID:

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

Detailed information for vg1218161842:

Variant ID: vg1218161842 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18161842
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACGCCCATTGGCCTATTGACGACGTTTTCTGATGTTGGTAGGAAAGCTTCGGCGATCTCTGCCCAGAGCGGCTATGAGGTGGCAACTAGCGGGACTGCC[G/A]
TTGTCGCCTCTCCTCGCGGGAAGTCCGCACCTGCTGCCGCAGAGTTCTCCGAGCCCGCGGCGGCGACCACGATTGCGGTGCCTTCGTCGGGGCCACAAGA

Reverse complement sequence

TCTTGTGGCCCCGACGAAGGCACCGCAATCGTGGTCGCCGCCGCGGGCTCGGAGAACTCTGCGGCAGCAGGTGCGGACTTCCCGCGAGGAGAGGCGACAA[C/T]
GGCAGTCCCGCTAGTTGCCACCTCATAGCCGCTCTGGGCAGAGATCGCCGAAGCTTTCCTACCAACATCAGAAAACGTCGTCAATAGGCCAATGGGCGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.20%	7.30%	0.23%	22.24%	NA
All Indica	2759	59.70%	5.60%	0.36%	34.29%	NA
All Japonica	1512	94.90%	4.80%	0.07%	0.26%	NA
Aus	269	34.20%	33.80%	0.00%	31.97%	NA
Indica I	595	92.30%	0.20%	0.00%	7.56%	NA
Indica II	465	54.80%	3.00%	0.43%	41.72%	NA
Indica III	913	43.60%	10.80%	0.66%	44.91%	NA
Indica Intermediate	786	56.70%	5.20%	0.25%	37.79%	NA
Temperate Japonica	767	99.30%	0.30%	0.00%	0.39%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	20.70%	0.41%	0.41%	NA
VI/Aromatic	96	75.00%	17.70%	0.00%	7.29%	NA
Intermediate	90	80.00%	11.10%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218161842	G -> DEL	LOC_Os12g30270.1	N	frameshift_variant	Average:53.858; most accessible tissue: Zhenshan97 young leaf, score: 83.199	N	N	N	N
vg1218161842	G -> A	LOC_Os12g30270.1	missense_variant ; p.Val134Ile; MODERATE	nonsynonymous_codon ; V134I	Average:53.858; most accessible tissue: Zhenshan97 young leaf, score: 83.199	unknown	unknown	TOLERATED	0.15

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218161842	2.64E-06	2.64E-06	mr1025	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
vg1218161842	NA	2.96E-06	mr1028	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
vg1218161842	4.55E-07	2.42E-08	mr1066	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
vg1218161842	NA	9.09E-09	mr1559	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
vg1218161842	2.24E-06	6.65E-10	mr1866	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