Search for Variation information by Variation ID:

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

Detailed information for vg0714958893:

Variant ID: vg0714958893 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14958893
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTGAAAAACTAATCTTTACTCGGATACCAAAAATTACATTTGTCGTCCCGGTTCGAATGAAAAAGGGACTAAAAATCGTTTTCCCACAATAGCTGTCA[C/T]
GCCTCCAACCGGTTAGTTTTGGTTACCAACCGGGACTAAAGATTAACGATCTTTAGTCCAAGTTGATATCACCAATCCGGACTAAAAATTGATTTTTAGA

Reverse complement sequence

TCTAAAAATCAATTTTTAGTCCGGATTGGTGATATCAACTTGGACTAAAGATCGTTAATCTTTAGTCCCGGTTGGTAACCAAAACTAACCGGTTGGAGGC[G/A]
TGACAGCTATTGTGGGAAAACGATTTTTAGTCCCTTTTTCATTCGAACCGGGACGACAAATGTAATTTTTGGTATCCGAGTAAAGATTAGTTTTTCAGTA

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	40.10%	4.80%	5.95%	49.07%	NA
All Indica	2759	7.20%	5.20%	8.52%	79.09%	NA
All Japonica	1512	98.80%	0.00%	0.33%	0.86%	NA
Aus	269	26.80%	30.50%	12.64%	30.11%	NA
Indica I	595	8.20%	6.20%	5.55%	80.00%	NA
Indica II	465	4.30%	1.50%	5.16%	89.03%	NA
Indica III	913	6.40%	5.80%	8.98%	78.86%	NA
Indica Intermediate	786	9.00%	6.00%	12.21%	72.77%	NA
Temperate Japonica	767	98.30%	0.00%	0.65%	1.04%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	86.50%	1.00%	2.08%	10.42%	NA
Intermediate	90	55.60%	2.20%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714958893	C -> DEL	N	N	silent_mutation	Average:66.483; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N
vg0714958893	C -> T	LOC_Os07g26070.1	downstream_gene_variant ; 1306.0bp to feature; MODIFIER	silent_mutation	Average:66.483; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N
vg0714958893	C -> T	LOC_Os07g26060-LOC_Os07g26070	intergenic_region ; MODIFIER	silent_mutation	Average:66.483; most accessible tissue: Minghui63 flag leaf, score: 79.676	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714958893	1.94E-06	NA	mr1934	Ind_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