Search for Variation information by Variation ID:

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

Detailed information for vg0818939785:

Variant ID: vg0818939785 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18939785
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATAATCCAAATAAAAAAGTCAAGTGTGTCATGCATTAGAAAAATAGAGACAATAGTTCCACTGCTAGATAGAAGGTGGTATGGCATATATAGTTTTGA[G/C]
CTTTTGACTGTACACCAATAAAACAACACGGATTCATGTGCCGGTTGCTCGTTACAATTTTGTCATGAATGCTCACTTTATGAATGAACAATGCAGCTGA

Reverse complement sequence

TCAGCTGCATTGTTCATTCATAAAGTGAGCATTCATGACAAAATTGTAACGAGCAACCGGCACATGAATCCGTGTTGTTTTATTGGTGTACAGTCAAAAG[C/G]
TCAAAACTATATATGCCATACCACCTTCTATCTAGCAGTGGAACTATTGTCTCTATTTTTCTAATGCATGACACACTTGACTTTTTTATTTGGATTATTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	0.70%	1.16%	18.37%	NA
All Indica	2759	74.20%	0.00%	0.83%	24.94%	NA
All Japonica	1512	84.80%	2.10%	1.85%	11.31%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	94.50%	0.00%	0.17%	5.38%	NA
Indica II	465	92.00%	0.00%	0.43%	7.53%	NA
Indica III	913	54.70%	0.00%	1.53%	43.81%	NA
Indica Intermediate	786	71.10%	0.00%	0.76%	28.12%	NA
Temperate Japonica	767	92.80%	3.90%	3.26%	0.00%	NA
Tropical Japonica	504	68.50%	0.00%	0.60%	30.95%	NA
Japonica Intermediate	241	93.40%	0.40%	0.00%	6.22%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	91.10%	0.00%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818939785	G -> C	LOC_Os08g30710.1	intron_variant ; MODIFIER	silent_mutation	Average:30.025; most accessible tissue: Callus, score: 62.286	N	N	N	N
vg0818939785	G -> DEL	N	N	silent_mutation	Average:30.025; most accessible tissue: Callus, score: 62.286	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818939785	3.25E-06	3.25E-06	mr1081_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
vg0818939785	NA	1.10E-06	mr1298_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
vg0818939785	NA	5.35E-06	mr1318_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
vg0818939785	NA	9.51E-07	mr1510_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
vg0818939785	NA	1.03E-07	mr1702_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
vg0818939785	NA	2.37E-06	mr1731_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