Search for Variation information by Variation ID:

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

Detailed information for vg0507593806:

Variant ID: vg0507593806 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7593806
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGGAGTAGATGACAACGCGTTTTCGAATTATTTGCCAACTGCATTGAAAGGCTCTGCACGTTCATGGCTGATGCATCTCCCGCCCTACTCGATTTCTT[C/T]
GTGGGCAGACCTGTGGCAGCAGTTCGTCGTCAACTTCCAAGGAACTTACAAGCGCCACGCTATCAAAGACGACCTACATGCGTTGACACAAAACCCAGGT

Reverse complement sequence

ACCTGGGTTTTGTGTCAACGCATGTAGGTCGTCTTTGATAGCGTGGCGCTTGTAAGTTCCTTGGAAGTTGACGACGAACTGCTGCCACAGGTCTGCCCAC[G/A]
AAGAAATCGAGTAGGGCGGGAGATGCATCAGCCATGAACGTGCAGAGCCTTTCAATGCAGTTGGCAAATAATTCGAAAACGCGTTGTCATCTACTCCGGT

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	59.00%	4.80%	7.87%	28.35%	NA
All Indica	2759	38.50%	2.00%	13.12%	46.47%	NA
All Japonica	1512	99.10%	0.10%	0.20%	0.60%	NA
Aus	269	25.30%	61.00%	2.23%	11.52%	NA
Indica I	595	32.80%	0.00%	17.82%	49.41%	NA
Indica II	465	40.90%	1.10%	8.39%	49.68%	NA
Indica III	913	38.00%	2.30%	15.12%	44.58%	NA
Indica Intermediate	786	41.90%	3.60%	10.05%	44.53%	NA
Temperate Japonica	767	98.80%	0.00%	0.39%	0.78%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	7.80%	1.11%	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
vg0507593806	C -> T	LOC_Os05g13710.1	upstream_gene_variant ; 1679.0bp to feature; MODIFIER	silent_mutation	Average:12.904; most accessible tissue: Callus, score: 43.244	N	N	N	N
vg0507593806	C -> T	LOC_Os05g13700.1	intron_variant ; MODIFIER	silent_mutation	Average:12.904; most accessible tissue: Callus, score: 43.244	N	N	N	N
vg0507593806	C -> DEL	N	N	silent_mutation	Average:12.904; most accessible tissue: Callus, score: 43.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507593806	NA	4.67E-06	mr1262	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
vg0507593806	NA	2.76E-06	mr1365	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
vg0507593806	4.49E-06	1.14E-07	mr1219_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