Search for Variation information by Variation ID:

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

Detailed information for vg0402068004:

Variant ID: vg0402068004 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2068004
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACTTGCTCCGGATACATGCAACATGAATTCATGATCATGGGTCTATTTTCTATGCTCAAAGACTGGACTATTTATTATTCCCCGTAAGGGTTATCAAC[T/C]
GAATACTTGTGCCAGTCGGAATTCAATTGTTATATCTATTTTGGAGTATCCCATAAAGGATAATCACTCAGATCAGAAGCTATTCATATGAGCTACACTT

Reverse complement sequence

AAGTGTAGCTCATATGAATAGCTTCTGATCTGAGTGATTATCCTTTATGGGATACTCCAAAATAGATATAACAATTGAATTCCGACTGGCACAAGTATTC[A/G]
GTTGATAACCCTTACGGGGAATAATAAATAGTCCAGTCTTTGAGCATAGAAAATAGACCCATGATCATGAATTCATGTTGCATGTATCCGGAGCAAGTCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.50%	1.40%	11.81%	7.32%	NA
All Indica	2759	80.40%	1.50%	12.43%	5.73%	NA
All Japonica	1512	75.10%	1.10%	12.10%	11.77%	NA
Aus	269	98.90%	0.40%	0.74%	0.00%	NA
Indica I	595	92.80%	0.50%	3.19%	3.53%	NA
Indica II	465	71.60%	1.70%	18.49%	8.17%	NA
Indica III	913	76.30%	2.20%	15.33%	6.13%	NA
Indica Intermediate	786	80.80%	1.30%	12.47%	5.47%	NA
Temperate Japonica	767	75.50%	0.90%	11.47%	12.13%	NA
Tropical Japonica	504	74.00%	1.80%	16.27%	7.94%	NA
Japonica Intermediate	241	75.90%	0.00%	5.39%	18.67%	NA
VI/Aromatic	96	69.80%	5.20%	20.83%	4.17%	NA
Intermediate	90	81.10%	1.10%	11.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402068004	T -> C	LOC_Os04g04380.1	upstream_gene_variant ; 1346.0bp to feature; MODIFIER	silent_mutation	Average:9.422; most accessible tissue: Callus, score: 21.49	N	N	N	N
vg0402068004	T -> C	LOC_Os04g04390.1	downstream_gene_variant ; 3045.0bp to feature; MODIFIER	silent_mutation	Average:9.422; most accessible tissue: Callus, score: 21.49	N	N	N	N
vg0402068004	T -> C	LOC_Os04g04380-LOC_Os04g04390	intergenic_region ; MODIFIER	silent_mutation	Average:9.422; most accessible tissue: Callus, score: 21.49	N	N	N	N
vg0402068004	T -> DEL	N	N	silent_mutation	Average:9.422; most accessible tissue: Callus, score: 21.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402068004	3.65E-06	4.45E-08	mr1698	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
vg0402068004	NA	2.38E-06	mr1698_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