RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0219279605:

Variant ID: vg0219279605 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19279605
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGGTAGAAGGGATTGAGGTGGGATGGGATGGAGAACTTTCACGGACCATTAGGGCCGTCTGGCTCCCAGCGGCTAGCTCGCAGACGAGCGGAGGCGGCC[G/A]
TTCACGGAGGCGGAGGAGGTTGCAGACGAGGCGGCGGCCGGACGCGGAGGCGCGCGCGGCGGCGGTCGCGGACGAGGCGGCGGCCGCGCACGGAGGCGGA

Reverse complement sequence

TCCGCCTCCGTGCGCGGCCGCCGCCTCGTCCGCGACCGCCGCCGCGCGCGCCTCCGCGTCCGGCCGCCGCCTCGTCTGCAACCTCCTCCGCCTCCGTGAA[C/T]
GGCCGCCTCCGCTCGTCTGCGAGCTAGCCGCTGGGAGCCAGACGGCCCTAATGGTCCGTGAAAGTTCTCCATCCCATCCCACCTCAATCCCTTCTACCAA

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	96.30%	2.80%	0.97%	0.00%	NA
All Indica	2759	99.40%	0.30%	0.33%	0.00%	NA
All Japonica	1512	89.70%	7.90%	2.38%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.70%	0.20%	1.18%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.50%	0.25%	0.00%	NA
Temperate Japonica	767	94.00%	2.60%	3.39%	0.00%	NA
Tropical Japonica	504	93.80%	5.80%	0.40%	0.00%	NA
Japonica Intermediate	241	67.20%	29.50%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0219279605	G -> A	LOC_Os02g32560.1	upstream_gene_variant ; 453.0bp to feature; MODIFIER	silent_mutation	Average:59.435; most accessible tissue: Minghui63 young leaf, score: 81.195	N	N	N	N
vg0219279605	G -> A	LOC_Os02g32560-LOC_Os02g32570	intergenic_region ; MODIFIER	silent_mutation	Average:59.435; most accessible tissue: Minghui63 young leaf, score: 81.195	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
vg0219279605	NA	2.39E-07	mr1114	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
vg0219279605	NA	5.80E-08	mr1117	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
vg0219279605	NA	3.28E-06	mr1118	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
vg0219279605	NA	5.04E-07	mr1119	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
vg0219279605	NA	9.57E-07	mr1120	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
vg0219279605	NA	6.86E-09	mr1123	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
vg0219279605	NA	6.26E-06	mr1240	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
vg0219279605	NA	5.09E-09	mr1242	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
vg0219279605	6.66E-06	6.98E-09	mr1247	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
vg0219279605	NA	8.78E-07	mr1917	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

Showing 1 to 10 of 24 entries

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Search for Variation information by Variation ID:

Detailed information for vg0219279605:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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