Search for Variation information by Variation ID:

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

Detailed information for vg0617030325:

Variant ID: vg0617030325 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17030325
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTTCCATATATGTAATCCTTTCTTATCTCATTCCCATGTACTCCTATATATACCGGTCCCCTAAAGCTCAATATAAGTGTGTTAATATTCACAGTATT[C/T]
CTCTTCCTATACTATCCAACATGGTATCAGAGATCAGAGCGGGCGACCTAGAGCCGCCCCTCTCACGCTTCCGCCGCCGCTGCCCCCGGAAGTAACGATC

Reverse complement sequence

GATCGTTACTTCCGGGGGCAGCGGCGGCGGAAGCGTGAGAGGGGCGGCTCTAGGTCGCCCGCTCTGATCTCTGATACCATGTTGGATAGTATAGGAAGAG[G/A]
AATACTGTGAATATTAACACACTTATATTGAGCTTTAGGGGACCGGTATATATAGGAGTACATGGGAATGAGATAAGAAAGGATTACATATATGGAAGGA

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	92.50%	0.20%	2.09%	5.23%	NA
All Indica	2759	97.50%	0.20%	1.78%	0.51%	NA
All Japonica	1512	89.90%	0.20%	0.60%	9.33%	NA
Aus	269	54.60%	0.40%	14.87%	30.11%	NA
Indica I	595	95.00%	0.50%	3.53%	1.01%	NA
Indica II	465	98.10%	0.00%	1.72%	0.22%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	96.30%	0.40%	2.42%	0.89%	NA
Temperate Japonica	767	98.40%	0.30%	0.78%	0.52%	NA
Tropical Japonica	504	74.80%	0.00%	0.60%	24.60%	NA
Japonica Intermediate	241	94.20%	0.40%	0.00%	5.39%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617030325	C -> T	LOC_Os06g29690.1	upstream_gene_variant ; 4755.0bp to feature; MODIFIER	silent_mutation	Average:76.318; most accessible tissue: Callus, score: 95.704	N	N	N	N
vg0617030325	C -> T	LOC_Os06g29679.1	downstream_gene_variant ; 4.0bp to feature; MODIFIER	silent_mutation	Average:76.318; most accessible tissue: Callus, score: 95.704	N	N	N	N
vg0617030325	C -> T	LOC_Os06g29679-LOC_Os06g29690	intergenic_region ; MODIFIER	silent_mutation	Average:76.318; most accessible tissue: Callus, score: 95.704	N	N	N	N
vg0617030325	C -> DEL	N	N	silent_mutation	Average:76.318; most accessible tissue: Callus, score: 95.704	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617030325	NA	3.20E-06	mr1522_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
vg0617030325	NA	7.98E-27	mr1757_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
vg0617030325	NA	1.47E-17	mr1817_2	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