Search for Variation information by Variation ID:

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

Detailed information for vg0102555772:

Variant ID: vg0102555772 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2555772
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTGCGGCTAAAAAAACGTAAATACCTGGGAAATCCAGTACATAATCTCTCGTATATCTTAAACTAGGGGTAAAAATGTCATTTCAAATTTCTCTTGCT[G/A]
ACATGACAATCTAATTAGGAAAAATATCTCACTTATGTGGTATTTATGTAAAAAAAGAAGGAAGAGTGGCATCTCAGTAGTGCCACTCCGTAAGAGTTGC

Reverse complement sequence

GCAACTCTTACGGAGTGGCACTACTGAGATGCCACTCTTCCTTCTTTTTTTACATAAATACCACATAAGTGAGATATTTTTCCTAATTAGATTGTCATGT[C/T]
AGCAAGAGAAATTTGAAATGACATTTTTACCCCTAGTTTAAGATATACGAGAGATTATGTACTGGATTTCCCAGGTATTTACGTTTTTTTAGCCGCACGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.50%	11.00%	0.57%	35.93%	NA
All Indica	2759	54.00%	0.80%	0.65%	44.58%	NA
All Japonica	1512	52.80%	31.80%	0.20%	15.21%	NA
Aus	269	24.20%	0.00%	1.49%	74.35%	NA
Indica I	595	32.10%	1.30%	0.84%	65.71%	NA
Indica II	465	64.30%	0.90%	0.65%	34.19%	NA
Indica III	913	56.80%	0.00%	0.55%	42.61%	NA
Indica Intermediate	786	61.20%	1.10%	0.64%	37.02%	NA
Temperate Japonica	767	42.50%	53.60%	0.13%	3.78%	NA
Tropical Japonica	504	70.00%	1.00%	0.20%	28.77%	NA
Japonica Intermediate	241	49.40%	27.00%	0.41%	23.24%	NA
VI/Aromatic	96	71.90%	14.60%	0.00%	13.54%	NA
Intermediate	90	66.70%	3.30%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102555772	G -> A	LOC_Os01g05400.1	downstream_gene_variant ; 3651.0bp to feature; MODIFIER	silent_mutation	Average:43.322; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0102555772	G -> A	LOC_Os01g05410.1	downstream_gene_variant ; 1751.0bp to feature; MODIFIER	silent_mutation	Average:43.322; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0102555772	G -> A	LOC_Os01g05410-LOC_Os01g05420	intergenic_region ; MODIFIER	silent_mutation	Average:43.322; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg0102555772	G -> DEL	N	N	silent_mutation	Average:43.322; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102555772	NA	8.76E-08	mr1382	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
vg0102555772	NA	2.26E-06	mr1424	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
vg0102555772	NA	8.93E-07	mr1544	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
vg0102555772	NA	3.90E-07	mr1829	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
vg0102555772	NA	6.44E-08	mr1916	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
vg0102555772	NA	5.01E-07	mr1045_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
vg0102555772	NA	6.83E-06	mr1206_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
vg0102555772	NA	6.95E-09	mr1354_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
vg0102555772	9.89E-09	3.88E-12	mr1567_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
vg0102555772	NA	2.19E-08	mr1567_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
vg0102555772	NA	3.78E-07	mr1621_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
vg0102555772	NA	7.70E-06	mr1723_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
vg0102555772	NA	7.72E-10	mr1769_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
vg0102555772	6.78E-07	NA	mr1806_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
vg0102555772	2.62E-07	4.43E-15	mr1829_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
vg0102555772	NA	1.12E-06	mr1829_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
vg0102555772	1.62E-06	3.37E-20	mr1902_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
vg0102555772	NA	5.36E-07	mr1902_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