Search for Variation information by Variation ID:

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

Detailed information for vg0709142041:

Variant ID: vg0709142041 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9142041
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGGAAAGTGGATATTTTCCTTAACTGAGTTTGATCTTCGGTATGAGTCACTGAAGGCGATTAAGGGACAAGCTATAGCCGATTTTATTGTGGAACATC[G/C]
TGATGATTCAATCGGCTCGGTTGAAATGGTGCCATGGACTTTATTCTTTGATGGATCGGTGTGTACTCATGGTTGTGGTATCAGCCTAGTTATAATTTCC

Reverse complement sequence

GGAAATTATAACTAGGCTGATACCACAACCATGAGTACACACCGATCCATCAAAGAATAAAGTCCATGGCACCATTTCAACCGAGCCGATTGAATCATCA[C/G]
GATGTTCCACAATAAAATCGGCTATAGCTTGTCCCTTAATCGCCTTCAGTGACTCATACCGAAGATCAAACTCAGTTAAGGAAAATATCCACTTTCCAAC

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	87.90%	8.20%	1.50%	2.45%	NA
All Indica	2759	84.60%	13.90%	1.52%	0.00%	NA
All Japonica	1512	90.70%	0.00%	1.79%	7.54%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	50.10%	44.70%	5.21%	0.00%	NA
Indica II	465	94.00%	5.80%	0.22%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	87.70%	11.10%	1.27%	0.00%	NA
Temperate Japonica	767	91.30%	0.00%	1.69%	7.04%	NA
Tropical Japonica	504	89.70%	0.00%	2.58%	7.74%	NA
Japonica Intermediate	241	90.90%	0.00%	0.41%	8.71%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	93.30%	4.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709142041	G -> DEL	LOC_Os07g15740.1	N	frameshift_variant	Average:17.868; most accessible tissue: Minghui63 flag leaf, score: 39.69	N	N	N	N
vg0709142041	G -> C	LOC_Os07g15740.1	missense_variant ; p.Arg759Pro; MODERATE	nonsynonymous_codon ; R759P	Average:17.868; most accessible tissue: Minghui63 flag leaf, score: 39.69	probably damaging	2.273	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709142041	8.38E-06	NA	mr1689	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
vg0709142041	2.38E-06	2.85E-06	mr1689	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