Search for Variation information by Variation ID:

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

Detailed information for vg0723903178:

Variant ID: vg0723903178 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23903178
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAGTAACAAAACCTAATAAATCAATAACGGTGCAAATTTGCAAAACCATCCTTCAAACTTAATGGTCCTCCTCCCGTGTTGCTCATTTCCGGCGATAA[G/A]
CTGACCCGGCGGCAACCACGGCGGCCGGCGGCCGGCTTCGCTCGTCCTCGGCAGCACCGGTCTCCTGGACGGAGCCCGGCCGTGCGTCCTCCGCCGCCGA

Reverse complement sequence

TCGGCGGCGGAGGACGCACGGCCGGGCTCCGTCCAGGAGACCGGTGCTGCCGAGGACGAGCGAAGCCGGCCGCCGGCCGCCGTGGTTGCCGCCGGGTCAG[C/T]
TTATCGCCGGAAATGAGCAACACGGGAGGAGGACCATTAAGTTTGAAGGATGGTTTTGCAAATTTGCACCGTTATTGATTTATTAGGTTTTGTTACTTTG

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	97.40%	2.00%	0.59%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.04%	0.00%	NA
All Japonica	1512	92.50%	5.80%	1.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.30%	10.30%	3.39%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.50%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0723903178	G -> A	LOC_Os07g39860.1	missense_variant ; p.Ala123Val; MODERATE	nonsynonymous_codon ; A123V	Average:82.828; most accessible tissue: Callus, score: 89.718	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723903178	5.58E-07	5.57E-07	mr1577	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