Search for Variation information by Variation ID:

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

Detailed information for vg0317442324:

Variant ID: vg0317442324 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17442324
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCACTATCCTTTAATTTTCTAGTGTACTAGAAAAAACACCCGTGCGTTGTAACGGCTGAAGGTTATTTTAATCTTATTATTGCTTACGATTTAGTTAA[G/A]
ATGAAATTCACTGTTAGAATTCGCTTGGATATATATTTTTTTAGAAAATCATGAGCTGCAATAAAAAAATCAGATATCTCAAATTAGCATGCGAGTTTTT

Reverse complement sequence

AAAAACTCGCATGCTAATTTGAGATATCTGATTTTTTTATTGCAGCTCATGATTTTCTAAAAAAATATATATCCAAGCGAATTCTAACAGTGAATTTCAT[C/T]
TTAACTAAATCGTAAGCAATAATAAGATTAAAATAACCTTCAGCCGTTACAACGCACGGGTGTTTTTTCTAGTACACTAGAAAATTAAAGGATAGTGGGT

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	97.20%	2.70%	0.04%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	92.50%	7.40%	0.07%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	90.70%	9.30%	0.00%	0.00%	NA
Japonica Intermediate	241	76.30%	23.20%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0317442324	G -> A	LOC_Os03g30550.1	downstream_gene_variant ; 3374.0bp to feature; MODIFIER	silent_mutation	Average:67.497; most accessible tissue: Callus, score: 89.817	N	N	N	N
vg0317442324	G -> A	LOC_Os03g30550-LOC_Os03g30570	intergenic_region ; MODIFIER	silent_mutation	Average:67.497; most accessible tissue: Callus, score: 89.817	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317442324	7.65E-07	7.65E-07	mr1877_2	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