Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0724211584:

Variant ID: vg0724211584 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24211584
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, C: 0.27, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGCTCGTGGGACTAATCTAGGTTTCATTCTTTAACAAGTTTCTCCTGTTACTAACTAATTCTTATTTTCTTTTCATGATTTAGACGAGAACCGGGGTG[C/A]
AAGGGTGATGCTGATGGTTCGTTTTATTGGATCAATCGATCTATCATCTTTTGTCTTGTTGATTTTCGTTTTGCCCTTATTTCTTCGTTCCCTGATAATG

Reverse complement sequence

CATTATCAGGGAACGAAGAAATAAGGGCAAAACGAAAATCAACAAGACAAAAGATGATAGATCGATTGATCCAATAAAACGAACCATCAGCATCACCCTT[G/T]
CACCCCGGTTCTCGTCTAAATCATGAAAAGAAAATAAGAATTAGTTAGTAACAGGAGAAACTTGTTAAAGAATGAAACCTAGATTAGTCCCACGAGCGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.00%	41.60%	0.06%	0.34%	NA
All Indica	2759	91.70%	7.90%	0.04%	0.33%	NA
All Japonica	1512	0.80%	99.00%	0.00%	0.20%	NA
Aus	269	45.40%	54.60%	0.00%	0.00%	NA
Indica I	595	93.10%	6.60%	0.00%	0.34%	NA
Indica II	465	88.00%	11.60%	0.00%	0.43%	NA
Indica III	913	97.00%	2.70%	0.00%	0.22%	NA
Indica Intermediate	786	86.60%	12.80%	0.13%	0.38%	NA
Temperate Japonica	767	0.70%	99.20%	0.00%	0.13%	NA
Tropical Japonica	504	0.40%	99.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.10%	0.00%	0.83%	NA
VI/Aromatic	96	44.80%	54.20%	0.00%	1.04%	NA
Intermediate	90	40.00%	54.40%	2.22%	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
vg0724211584	C -> DEL	LOC_Os07g40380.1	N	frameshift_variant	Average:42.847; most accessible tissue: Callus, score: 67.615	N	N	N	N
vg0724211584	C -> A	LOC_Os07g40380.1	missense_variant ; p.Ala20Glu; MODERATE	nonsynonymous_codon ; A20E	Average:42.847; most accessible tissue: Callus, score: 67.615	unknown	unknown	TOLERATED	0.26

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724211584	NA	2.04E-26	mr1181	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
vg0724211584	NA	1.55E-06	mr1408	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
vg0724211584	NA	4.16E-07	mr1761	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
vg0724211584	NA	2.20E-31	mr1878	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
vg0724211584	NA	6.70E-06	mr1181_2	Ind_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