Search for Variation information by Variation ID:

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

Detailed information for vg0505001004:

Variant ID: vg0505001004 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5001004
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATTATGGCTGCCTGTTTCTTTGGAAGGAATGTGACGAGGGTTTATTTGTAAAACAGTTTTTACTGTACGTGTAGATCCTAAAATTATATGCACCACAT[G/T]
ATCTCTTCTTGTGCTTATTCTTTATCTTTTTTCTTTTCTTTTCTTTCTTTCAATAACTTCATGCATATTCGAAAGTCTTGAATTTTACCATCCATCTAGC

Reverse complement sequence

GCTAGATGGATGGTAAAATTCAAGACTTTCGAATATGCATGAAGTTATTGAAAGAAAGAAAAGAAAAGAAAAAAGATAAAGAATAAGCACAAGAAGAGAT[C/A]
ATGTGGTGCATATAATTTTAGGATCTACACGTACAGTAAAAACTGTTTTACAAATAAACCCTCGTCACATTCCTTCCAAAGAAACAGGCAGCCATAATCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	13.20%	0.28%	0.00%	NA
All Indica	2759	96.90%	3.10%	0.00%	0.00%	NA
All Japonica	1512	87.80%	11.40%	0.79%	0.00%	NA
Aus	269	2.60%	97.00%	0.37%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	97.40%	2.60%	0.00%	0.00%	NA
Indica Intermediate	786	94.70%	5.30%	0.00%	0.00%	NA
Temperate Japonica	767	86.70%	11.90%	1.43%	0.00%	NA
Tropical Japonica	504	89.30%	10.50%	0.20%	0.00%	NA
Japonica Intermediate	241	88.00%	12.00%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505001004	G -> T	LOC_Os05g09020.1	upstream_gene_variant ; 1378.0bp to feature; MODIFIER	silent_mutation	Average:31.96; most accessible tissue: Callus, score: 61.075	N	N	N	N
vg0505001004	G -> T	LOC_Os05g09020.2	upstream_gene_variant ; 1375.0bp to feature; MODIFIER	silent_mutation	Average:31.96; most accessible tissue: Callus, score: 61.075	N	N	N	N
vg0505001004	G -> T	LOC_Os05g09020-LOC_Os05g09030	intergenic_region ; MODIFIER	silent_mutation	Average:31.96; most accessible tissue: Callus, score: 61.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505001004	NA	4.71E-07	mr1057	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
vg0505001004	NA	7.74E-08	mr1403	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
vg0505001004	NA	1.23E-08	mr1057_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
vg0505001004	NA	8.69E-08	mr1126_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
vg0505001004	NA	7.60E-09	mr1166_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
vg0505001004	NA	1.64E-06	mr1456_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
vg0505001004	NA	8.79E-08	mr1465_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
vg0505001004	NA	1.51E-06	mr1577_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
vg0505001004	NA	4.33E-14	mr1583_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
vg0505001004	6.81E-07	6.81E-07	mr1587_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
vg0505001004	NA	2.30E-06	mr1792_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
vg0505001004	NA	2.23E-06	mr1929_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