RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0407782850:

Variant ID: vg0407782850 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7782850
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTCTGGTCTCCGTGGATTATCCGGATTTCCAGCGTCTGGTGGACAAGAGCATCCGCTTGGAAGCCAAGCACAAGGAACTGGAGTCGCACAAGCGTCGC[T/C]
TGGTGAATTTCCGCAATCAACAGGGGGCTAACCAAAGGGTCTGCTACACCAATCCCTATCCAGGTGGATCCTCCTCGCTGCAGCAGCAGCAACCTCGCTC

Reverse complement sequence

GAGCGAGGTTGCTGCTGCTGCAGCGAGGAGGATCCACCTGGATAGGGATTGGTGTAGCAGACCCTTTGGTTAGCCCCCTGTTGATTGCGGAAATTCACCA[A/G]
GCGACGCTTGTGCGACTCCAGTTCCTTGTGCTTGGCTTCCAAGCGGATGCTCTTGTCCACCAGACGCTGGAAATCCGGATAATCCACGGAGACCAGACGC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.50%	6.90%	13.18%	4.38%	NA
All Indica	2759	76.30%	7.10%	16.31%	0.36%	NA
All Japonica	1512	81.70%	0.50%	5.09%	12.63%	NA
Aus	269	31.20%	43.50%	24.16%	1.12%	NA
Indica I	595	63.40%	7.90%	28.74%	0.00%	NA
Indica II	465	77.20%	6.70%	14.62%	1.51%	NA
Indica III	913	83.20%	7.30%	9.20%	0.22%	NA
Indica Intermediate	786	77.40%	6.40%	16.16%	0.13%	NA
Temperate Japonica	767	97.70%	0.00%	0.26%	2.09%	NA
Tropical Japonica	504	55.40%	1.40%	12.70%	30.56%	NA
Japonica Intermediate	241	86.30%	0.40%	4.56%	8.71%	NA
VI/Aromatic	96	70.80%	4.20%	25.00%	0.00%	NA
Intermediate	90	86.70%	2.20%	7.78%	3.33%	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
vg0407782850	T -> C	LOC_Os04g13930.1	synonymous_variant ; p.Leu480Leu; LOW	synonymous_codon	Average:13.23; most accessible tissue: Callus, score: 30.616	N	N	N	N
vg0407782850	T -> DEL	LOC_Os04g13930.1	N	frameshift_variant	Average:13.23; most accessible tissue: Callus, score: 30.616	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407782850	NA	1.06E-09	mr1118	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
vg0407782850	NA	4.48E-06	mr1496	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
vg0407782850	1.66E-06	4.51E-15	mr1118_2	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
vg0407782850	NA	7.55E-07	mr1496_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

Showing 1 to 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0407782850:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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