Search for Variation information by Variation ID:

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

Detailed information for vg0501601241:

Variant ID: vg0501601241 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1601241
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGAGCTCCGTTTAAGCCCATTCAAGTCTCAGTAAATCAAGAAAAATGTGTAGAATCCATTAAAAATAGTTTTGTTCCCTGTTTCAGTAGTCTTATAGC[C/T]
TGTTTGCATTGTTTGCCTTGTATGTCGCTAGATTTCGGTTCCTCCGACGCTCCGGTGTACTTTGAAATAGTCGCCGAGGTTCCTCCAGCAGTAGAGCAAG

Reverse complement sequence

CTTGCTCTACTGCTGGAGGAACCTCGGCGACTATTTCAAAGTACACCGGAGCGTCGGAGGAACCGAAATCTAGCGACATACAAGGCAAACAATGCAAACA[G/A]
GCTATAAGACTACTGAAACAGGGAACAAAACTATTTTTAATGGATTCTACACATTTTTCTTGATTTACTGAGACTTGAATGGGCTTAAACGGAGCTCGGA

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	60.00%	3.00%	6.18%	30.74%	NA
All Indica	2759	48.70%	0.40%	6.78%	44.07%	NA
All Japonica	1512	88.20%	8.70%	0.46%	2.65%	NA
Aus	269	14.50%	0.00%	33.46%	52.04%	NA
Indica I	595	39.50%	0.00%	2.18%	58.32%	NA
Indica II	465	43.90%	1.50%	10.32%	44.30%	NA
Indica III	913	59.70%	0.00%	8.98%	31.33%	NA
Indica Intermediate	786	45.90%	0.50%	5.60%	47.96%	NA
Temperate Japonica	767	82.00%	16.60%	0.26%	1.17%	NA
Tropical Japonica	504	95.20%	0.20%	0.79%	3.77%	NA
Japonica Intermediate	241	92.90%	1.70%	0.41%	4.98%	NA
VI/Aromatic	96	61.50%	0.00%	2.08%	36.46%	NA
Intermediate	90	67.80%	1.10%	6.67%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0501601241	C -> T	LOC_Os05g03680.1	upstream_gene_variant ; 364.0bp to feature; MODIFIER	silent_mutation	Average:9.929; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0501601241	C -> T	LOC_Os05g03690.1	upstream_gene_variant ; 1990.0bp to feature; MODIFIER	silent_mutation	Average:9.929; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0501601241	C -> T	LOC_Os05g03680-LOC_Os05g03690	intergenic_region ; MODIFIER	silent_mutation	Average:9.929; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0501601241	C -> DEL	N	N	silent_mutation	Average:9.929; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501601241	4.18E-06	4.18E-06	mr1054	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
vg0501601241	NA	2.79E-06	mr1171	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
vg0501601241	NA	4.16E-06	mr1358	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
vg0501601241	4.68E-06	4.68E-06	mr1899	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
vg0501601241	4.37E-06	4.37E-06	mr1941	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
vg0501601241	2.59E-06	2.58E-06	mr1472_2	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