Search for Variation information by Variation ID:

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

Detailed information for vg0723700693:

Variant ID: vg0723700693 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23700693
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GGATCGTTGGGTCGAAAGATCCACACACCTCCTCCGAAGACCCAAAAGAAAAAAAGAAGTCCTACCACGTCGAGGCAACAGTGGAGAGGAATCAACCACC[G/C]
TCATCGAGGCAAGAAACAAAAAGGAGCAACATTAAATTGATTGAGGAAACGATGAGACGACGATGAATGCGAGTGGCGAACTAGGAGGCAGAGGTGGCAA

Reverse complement sequence

TTGCCACCTCTGCCTCCTAGTTCGCCACTCGCATTCATCGTCGTCTCATCGTTTCCTCAATCAATTTAATGTTGCTCCTTTTTGTTTCTTGCCTCGATGA[C/G]
GGTGGTTGATTCCTCTCCACTGTTGCCTCGACGTGGTAGGACTTCTTTTTTTCTTTTGGGTCTTCGGAGGAGGTGTGTGGATCTTTCGACCCAACGATCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.90%	15.30%	0.70%	3.11%	NA
All Indica	2759	96.40%	3.30%	0.18%	0.11%	NA
All Japonica	1512	49.20%	39.80%	1.65%	9.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.20%	0.34%	0.00%	NA
Indica II	465	94.40%	5.40%	0.00%	0.22%	NA
Indica III	913	98.50%	1.10%	0.22%	0.22%	NA
Indica Intermediate	786	93.50%	6.40%	0.13%	0.00%	NA
Temperate Japonica	767	74.80%	20.30%	1.17%	3.65%	NA
Tropical Japonica	504	22.80%	58.70%	2.78%	15.67%	NA
Japonica Intermediate	241	22.80%	62.20%	0.83%	14.11%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	78.90%	14.40%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0723700693	G -> DEL	N	N	silent_mutation	Average:70.35; most accessible tissue: Callus, score: 90.664	N	N	N	N
vg0723700693	G -> C	LOC_Os07g39560.1	upstream_gene_variant ; 3461.0bp to feature; MODIFIER	silent_mutation	Average:70.35; most accessible tissue: Callus, score: 90.664	N	N	N	N
vg0723700693	G -> C	LOC_Os07g39560.3	upstream_gene_variant ; 3461.0bp to feature; MODIFIER	silent_mutation	Average:70.35; most accessible tissue: Callus, score: 90.664	N	N	N	N
vg0723700693	G -> C	LOC_Os07g39560.2	upstream_gene_variant ; 4229.0bp to feature; MODIFIER	silent_mutation	Average:70.35; most accessible tissue: Callus, score: 90.664	N	N	N	N
vg0723700693	G -> C	LOC_Os07g39550-LOC_Os07g39560	intergenic_region ; MODIFIER	silent_mutation	Average:70.35; most accessible tissue: Callus, score: 90.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723700693	NA	3.00E-11	Awn_length	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0723700693	NA	2.35E-08	mr1354	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
vg0723700693	NA	2.48E-09	mr1354_2	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
vg0723700693	NA	3.34E-06	mr1870_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