RiceVarMap2

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Detailed information for vg0234907559:

Variant ID: vg0234907559 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34907559
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, C: 0.26, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GAGATGGGATGAAAACCCAAATAGGGAGGAAGCTAATGCCTTAAGCTTATTGTCAGTAAAACCACAACTGTTGAACAAGTCACTCATAAGGTTTCAGTTT[A/C]
ATTGTTCAGAAAACAAACAAAAAGGAGGACAAATATGGCACTGATAGATCACCAAAAATCAACATGGCCTGGACATTCATCATAGCTTCTCAACTTAAAA

Reverse complement sequence

TTTTAAGTTGAGAAGCTATGATGAATGTCCAGGCCATGTTGATTTTTGGTGATCTATCAGTGCCATATTTGTCCTCCTTTTTGTTTGTTTTCTGAACAAT[T/G]
AAACTGAAACCTTATGAGTGACTTGTTCAACAGTTGTGGTTTTACTGACAATAAGCTTAAGGCATTAGCTTCCTCCCTATTTGGGTTTTCATCCCATCTC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	28.40%	0.02%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	19.40%	80.50%	0.07%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.90%	1.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	8.10%	91.90%	0.00%	0.00%	NA
Tropical Japonica	504	42.10%	57.70%	0.20%	0.00%	NA
Japonica Intermediate	241	8.30%	91.70%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	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
vg0234907559	A -> C	LOC_Os02g56950.1	3_prime_UTR_variant ; 322.0bp to feature; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N
vg0234907559	A -> C	LOC_Os02g56960.1	upstream_gene_variant ; 3471.0bp to feature; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N
vg0234907559	A -> C	LOC_Os02g56940.1	downstream_gene_variant ; 3656.0bp to feature; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N
vg0234907559	A -> C	LOC_Os02g56940.2	downstream_gene_variant ; 3656.0bp to feature; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N
vg0234907559	A -> C	LOC_Os02g56940.3	downstream_gene_variant ; 3656.0bp to feature; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N
vg0234907559	A -> C	LOC_Os02g56950.2	intron_variant ; MODIFIER	silent_mutation	Average:55.896; most accessible tissue: Callus, score: 96.356	N	N	N	N

Showing 1 to 6 of 6 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234907559	NA	1.41E-12	Grain_width	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0234907559	NA	7.59E-06	mr1125	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
vg0234907559	NA	1.44E-10	mr1188	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
vg0234907559	NA	8.26E-07	mr1278	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
vg0234907559	NA	1.58E-08	mr1302	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
vg0234907559	NA	5.52E-14	mr1376	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
vg0234907559	NA	8.33E-07	mr1392	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
vg0234907559	NA	5.52E-14	mr1431	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
vg0234907559	NA	2.03E-07	mr1471	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
vg0234907559	NA	6.79E-06	mr1642	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 19 entries

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Search for Variation information by Variation ID:

Detailed information for vg0234907559:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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