Search for Variation information by Variation ID:

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

Detailed information for vg0505539259:

Variant ID: vg0505539259 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5539259
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAGAGGGCTGCTACAAAACGGGATCCCGTTACAACGGGATAGACATATTAACTATTTTCTTGCACGAGTATCACAGGTATCAGGTCTTAGGTATCACAG[A/G]
TACCAAGTAACAGGTATCGTAGAAATCGGGTACCATGTAGCTGGTACCATAACATGTATCATGTATAGGTACTGTCTCATAGAAGAGTATCCCGTTCCAA

Reverse complement sequence

TTGGAACGGGATACTCTTCTATGAGACAGTACCTATACATGATACATGTTATGGTACCAGCTACATGGTACCCGATTTCTACGATACCTGTTACTTGGTA[T/C]
CTGTGATACCTAAGACCTGATACCTGTGATACTCGTGCAAGAAAATAGTTAATATGTCTATCCCGTTGTAACGGGATCCCGTTTTGTAGCAGCCCTCTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.60%	27.40%	0.00%	0.00%	NA
All Indica	2759	92.50%	7.50%	0.00%	0.00%	NA
All Japonica	1512	46.30%	53.70%	0.00%	0.00%	NA
Aus	269	15.20%	84.80%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	92.30%	7.70%	0.00%	0.00%	NA
Indica III	913	91.70%	8.30%	0.00%	0.00%	NA
Indica Intermediate	786	88.80%	11.20%	0.00%	0.00%	NA
Temperate Japonica	767	70.40%	29.60%	0.00%	0.00%	NA
Tropical Japonica	504	12.10%	87.90%	0.00%	0.00%	NA
Japonica Intermediate	241	41.10%	58.90%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	60.00%	40.00%	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
vg0505539259	A -> G	LOC_Os05g09740.1	upstream_gene_variant ; 3149.0bp to feature; MODIFIER	silent_mutation	Average:64.704; most accessible tissue: Callus, score: 83.682	N	N	N	N
vg0505539259	A -> G	LOC_Os05g09740-LOC_Os05g10210	intergenic_region ; MODIFIER	silent_mutation	Average:64.704; most accessible tissue: Callus, score: 83.682	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505539259	NA	3.51E-07	mr1206	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
vg0505539259	NA	1.67E-08	mr1260	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
vg0505539259	4.19E-06	NA	mr1697	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
vg0505539259	9.29E-09	8.52E-10	mr1697	Ind_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
vg0505539259	NA	5.19E-09	mr1757	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
vg0505539259	NA	1.31E-07	mr1002_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
vg0505539259	NA	1.31E-07	mr1010_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
vg0505539259	NA	2.31E-06	mr1011_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
vg0505539259	NA	1.40E-07	mr1013_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
vg0505539259	NA	7.61E-06	mr1263_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
vg0505539259	NA	8.98E-06	mr1346_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
vg0505539259	NA	2.25E-08	mr1363_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
vg0505539259	NA	7.04E-08	mr1502_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
vg0505539259	NA	5.48E-07	mr1668_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
vg0505539259	NA	2.24E-06	mr1757_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