Search for Variation information by Variation ID:

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

Detailed information for vg0712046729:

Variant ID: vg0712046729 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12046729
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGATCTGTGTGACTTGCCTTGCTGGCCTTGGAATTCCTCAAAATCTTCTCCTGCAAAATCGGACTTTCCGGGAACGTCGGAATCTAAAGAGAAAAGAA[A/C]
AAAATCACTAAAACAGCACATAAACAAGCATGAACAATACATGTGGATATTTTTAACATGTAGATCTCAATTTTAGAAAAATTTAAAGACTTGAACCAAC

Reverse complement sequence

GTTGGTTCAAGTCTTTAAATTTTTCTAAAATTGAGATCTACATGTTAAAAATATCCACATGTATTGTTCATGCTTGTTTATGTGCTGTTTTAGTGATTTT[T/G]
TTCTTTTCTCTTTAGATTCCGACGTTCCCGGAAAGTCCGATTTTGCAGGAGAAGATTTTGAGGAATTCCAAGGCCAGCAAGGCAAGTCACACAGATCCCA

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	63.00%	15.50%	3.81%	17.69%	NA
All Indica	2759	93.50%	1.80%	3.48%	1.23%	NA
All Japonica	1512	10.60%	41.60%	0.79%	46.96%	NA
Aus	269	56.50%	11.90%	24.54%	7.06%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	93.50%	3.00%	2.80%	0.65%	NA
Indica III	913	95.80%	0.00%	3.83%	0.33%	NA
Indica Intermediate	786	85.90%	4.50%	6.11%	3.56%	NA
Temperate Japonica	767	6.80%	55.40%	0.65%	37.16%	NA
Tropical Japonica	504	17.10%	25.20%	0.99%	56.75%	NA
Japonica Intermediate	241	9.50%	32.00%	0.83%	57.68%	NA
VI/Aromatic	96	27.10%	4.20%	3.12%	65.62%	NA
Intermediate	90	63.30%	22.20%	3.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712046729	A -> DEL	N	N	silent_mutation	Average:29.454; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0712046729	A -> C	LOC_Os07g20830.1	upstream_gene_variant ; 636.0bp to feature; MODIFIER	silent_mutation	Average:29.454; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0712046729	A -> C	LOC_Os07g20820.1	downstream_gene_variant ; 2117.0bp to feature; MODIFIER	silent_mutation	Average:29.454; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0712046729	A -> C	LOC_Os07g20820-LOC_Os07g20830	intergenic_region ; MODIFIER	silent_mutation	Average:29.454; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712046729	4.96E-06	3.04E-09	mr1915	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