Search for Variation information by Variation ID:

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

Detailed information for vg0106157133:

Variant ID: vg0106157133 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6157133
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCAGTGTGACGCACGGTTTATTTCGCTACGGTTTTCGTTAATAGCATGTCGGTCCTAGCTAG[C/A]
TTTTCTAATTCTGCATAACAACCATAGTAATCATATTTCGAGATCCATCGATTGGCACGAGCCAATGAAAAAAACTAAAATTTAAATTTTTAAATTTGAT

Reverse complement sequence

ATCAAATTTAAAAATTTAAATTTTAGTTTTTTTCATTGGCTCGTGCCAATCGATGGATCTCGAAATATGATTACTATGGTTGTTATGCAGAATTAGAAAA[G/T]
CTAGCTAGGACCGACATGCTATTAACGAAAACCGTAGCGAAATAAACCGTGCGTCACACTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.40%	0.50%	1.04%	15.07%	NA
All Indica	2759	92.00%	0.00%	0.14%	7.87%	NA
All Japonica	1512	84.50%	1.40%	2.78%	11.38%	NA
Aus	269	1.90%	0.00%	0.37%	97.77%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	78.70%	0.00%	0.43%	20.86%	NA
Indica III	913	94.90%	0.00%	0.00%	5.15%	NA
Indica Intermediate	786	90.50%	0.00%	0.25%	9.29%	NA
Temperate Japonica	767	90.10%	2.10%	4.56%	3.26%	NA
Tropical Japonica	504	93.30%	0.00%	0.40%	6.35%	NA
Japonica Intermediate	241	48.10%	2.10%	2.07%	47.72%	NA
VI/Aromatic	96	46.90%	2.10%	1.04%	50.00%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0106157133	C -> A	LOC_Os01g11430-LOC_Os01g11450	intergenic_region ; MODIFIER	silent_mutation	Average:59.586; most accessible tissue: Callus, score: 83.023	N	N	N	N
vg0106157133	C -> DEL	N	N	silent_mutation	Average:59.586; most accessible tissue: Callus, score: 83.023	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106157133	2.36E-06	7.82E-07	mr1057	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
vg0106157133	4.51E-06	4.43E-06	mr1062	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
vg0106157133	NA	9.33E-06	mr1677	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