RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0118996593:

Variant ID: vg0118996593 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18996593
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CATGCCGGAGCACGAAGCGTCCACCGCTGCGTCGTACACCTCCTACGAGAGGCGGAGCCTTGCACCGCCGCCGCAAGAACACTCCATTCTCGAGTGGGAG[A/T]
TCTCGTTGCCGCTCCCAGGCGTGGCAGCAACCGCCGTCGAGAGAGAATATAGAGAGAGATGAGAAGAGAGATACGAGATAGAGCTGACATGTGGGCACAA

Reverse complement sequence

TTGTGCCCACATGTCAGCTCTATCTCGTATCTCTCTTCTCATCTCTCTCTATATTCTCTCTCGACGGCGGTTGCTGCCACGCCTGGGAGCGGCAACGAGA[T/A]
CTCCCACTCGAGAATGGAGTGTTCTTGCGGCGGCGGTGCAAGGCTCCGCCTCTCGTAGGAGGTGTACGACGCAGCGGTGGACGCTTCGTGCTCCGGCATG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.50%	28.30%	0.19%	0.00%	NA
All Indica	2759	95.40%	4.50%	0.11%	0.00%	NA
All Japonica	1512	30.70%	69.00%	0.33%	0.00%	NA
Aus	269	75.80%	24.20%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	95.70%	3.90%	0.43%	0.00%	NA
Indica III	913	92.70%	7.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.00%	4.80%	0.13%	0.00%	NA
Temperate Japonica	767	14.10%	85.50%	0.39%	0.00%	NA
Tropical Japonica	504	41.30%	58.50%	0.20%	0.00%	NA
Japonica Intermediate	241	61.40%	38.20%	0.41%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	56.70%	42.20%	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
vg0118996593	A -> T	LOC_Os01g34450.1	downstream_gene_variant ; 1619.0bp to feature; MODIFIER	silent_mutation	Average:68.208; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0118996593	A -> T	LOC_Os01g34450-LOC_Os01g34460	intergenic_region ; MODIFIER	silent_mutation	Average:68.208; most accessible tissue: Zhenshan97 panicle, score: 83.904	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
vg0118996593	NA	4.75E-06	mr1063	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
vg0118996593	NA	1.67E-06	mr1183	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
vg0118996593	NA	6.91E-06	mr1794	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
vg0118996593	NA	5.94E-15	mr1118_2	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
vg0118996593	NA	5.35E-13	mr1496_2	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 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0118996593:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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