RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1126042091:

Variant ID: vg1126042091 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26042091
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGGAAATATGGGAACTGGACTATGGCCTGAACATCCAGATCCTTGTGCTCCGTTGTGAATGGGTTAAAGACACAATAGGAGTTTCCGTTGATGACTAC[G/A]
GGCTAACAATAGTCGATCACAGTAAAACAGGCCACAAGGATGATCCATGGGTTTTAGCAGAGCGTGTGGCTCAAGTGTTTTATGTGAAGGACCCTTCGGA

Reverse complement sequence

TCCGAAGGGTCCTTCACATAAAACACTTGAGCCACACGCTCTGCTAAAACCCATGGATCATCCTTGTGGCCTGTTTTACTGTGATCGACTATTGTTAGCC[C/T]
GTAGTCATCAACGGAAACTCCTATTGTGTCTTTAACCCATTCACAACGGAGCACAAGGATCTGGATGTTCAGGCCATAGTCCAGTTCCCATATTTCCTGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.10%	8.40%	2.01%	0.51%	NA
All Indica	2759	88.80%	9.50%	0.80%	0.87%	NA
All Japonica	1512	86.70%	8.50%	4.76%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.30%	1.01%	0.00%	NA
Indica II	465	94.80%	4.70%	0.22%	0.22%	NA
Indica III	913	78.20%	19.70%	0.00%	2.08%	NA
Indica Intermediate	786	90.10%	7.50%	1.91%	0.51%	NA
Temperate Japonica	767	82.70%	10.40%	6.91%	0.00%	NA
Tropical Japonica	504	95.80%	4.00%	0.20%	0.00%	NA
Japonica Intermediate	241	80.50%	12.00%	7.47%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	1.11%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126042091	G -> A	LOC_Os11g43150.1	missense_variant ; p.Gly625Arg; MODERATE	nonsynonymous_codon ; G625R	Average:31.427; most accessible tissue: Minghui63 young leaf, score: 51.901	probably damaging	2.607	DELETERIOUS	0.02
vg1126042091	G -> DEL	LOC_Os11g43150.1	N	frameshift_variant	Average:31.427; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126042091	NA	6.73E-06	mr1006	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
vg1126042091	9.56E-06	3.04E-07	mr1007	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
vg1126042091	7.31E-06	NA	mr1624	Jap_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

Showing 1 to 3 of 3 entries

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Search for Variation information by Variation ID:

Detailed information for vg1126042091:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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