Search for Variation information by Variation ID:

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

Detailed information for vg0402701254:

Variant ID: vg0402701254 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2701254
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCGAAAGAGTTCGGGTATGGCTCTAGTATCTTTTCTATCGGCTTTTGTAAGACTTCCAGCATTAATGAAATATTCTTCTTTATATACTTTCGGTACTTT[G/T]
TTTAGTCTGAGTATCGGCTTTACTTTACATTTGTGTCGTATTAATTGTATGGTTAGCTTCCCAGAGTGGTATTTATTAATGTAAACGAGGTACTTAGATT

Reverse complement sequence

AATCTAAGTACCTCGTTTACATTAATAAATACCACTCTGGGAAGCTAACCATACAATTAATACGACACAAATGTAAAGTAAAGCCGATACTCAGACTAAA[C/A]
AAAGTACCGAAAGTATATAAAGAAGAATATTTCATTAATGCTGGAAGTCTTACAAAAGCCGATAGAAAAGATACTAGAGCCATACCCGAACTCTTTCGAA

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	67.60%	16.30%	0.68%	15.38%	NA
All Indica	2759	67.30%	23.80%	0.83%	8.12%	NA
All Japonica	1512	62.90%	6.40%	0.46%	30.22%	NA
Aus	269	86.20%	0.70%	0.00%	13.01%	NA
Indica I	595	95.60%	3.90%	0.17%	0.34%	NA
Indica II	465	70.30%	14.60%	1.29%	13.76%	NA
Indica III	913	49.50%	39.90%	1.10%	9.53%	NA
Indica Intermediate	786	64.60%	25.60%	0.76%	9.03%	NA
Temperate Japonica	767	90.50%	0.80%	0.13%	8.60%	NA
Tropical Japonica	504	34.50%	7.30%	0.79%	57.34%	NA
Japonica Intermediate	241	34.40%	22.40%	0.83%	42.32%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	71.10%	17.80%	2.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402701254	G -> DEL	N	N	silent_mutation	Average:15.418; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0402701254	G -> T	LOC_Os04g05400.1	downstream_gene_variant ; 3868.0bp to feature; MODIFIER	silent_mutation	Average:15.418; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0402701254	G -> T	LOC_Os04g05380-LOC_Os04g05400	intergenic_region ; MODIFIER	silent_mutation	Average:15.418; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402701254	2.12E-06	5.28E-07	mr1037_2	Ind_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
vg0402701254	NA	4.03E-07	mr1458_2	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