Search for Variation information by Variation ID:

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

Detailed information for vg0122080523:

Variant ID: vg0122080523 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22080523
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCATATATATATATATTACTTTTCGATTTGATTAAATTACTTATTATACAATCATAATGTTGTGAGTTGTTTATTTTATTATCTTTTTTAGTCAATTC[C/T]
ATAATTTGTGCTGATTAAATTTAATTTTTAGATAGACTCACGTTTTTACCTCCATAACAGATCTATTTTTAATGTCATGACAAAGTTACTTCTTTTTTAT

Reverse complement sequence

ATAAAAAAGAAGTAACTTTGTCATGACATTAAAAATAGATCTGTTATGGAGGTAAAAACGTGAGTCTATCTAAAAATTAAATTTAATCAGCACAAATTAT[G/A]
GAATTGACTAAAAAAGATAATAAAATAAACAACTCACAACATTATGATTGTATAATAAGTAATTTAATCAAATCGAAAAGTAATATATATATATATGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.30%	17.40%	2.16%	0.17%	NA
All Indica	2759	73.90%	25.40%	0.47%	0.22%	NA
All Japonica	1512	87.80%	6.50%	5.69%	0.07%	NA
Aus	269	95.90%	3.00%	0.74%	0.37%	NA
Indica I	595	96.30%	3.40%	0.00%	0.34%	NA
Indica II	465	93.50%	5.40%	1.08%	0.00%	NA
Indica III	913	49.60%	49.80%	0.44%	0.11%	NA
Indica Intermediate	786	73.50%	25.60%	0.51%	0.38%	NA
Temperate Japonica	767	80.60%	10.70%	8.74%	0.00%	NA
Tropical Japonica	504	97.80%	0.60%	1.59%	0.00%	NA
Japonica Intermediate	241	89.60%	5.40%	4.56%	0.41%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0122080523	C -> T	LOC_Os01g39260.1	upstream_gene_variant ; 1733.0bp to feature; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0122080523	C -> T	LOC_Os01g39250.1	downstream_gene_variant ; 662.0bp to feature; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0122080523	C -> T	LOC_Os01g39250-LOC_Os01g39260	intergenic_region ; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0122080523	C -> DEL	N	N	silent_mutation	Average:27.503; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122080523	2.29E-06	2.29E-06	mr1505	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