RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0613848822:

Variant ID: vg0613848822 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13848822
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCCTGCAGTACTGGAGGGTTATAGTGATTCTAACTGGATCTCTGATGTGGATGAGATCAAAGCCACTAGTGGATATGTCTTCACACTGGATGGTGGTG[T/C]
TGTTTCGTGGAGGTCTTGCAAACAGACCATTTTGACGAGGTCAACCATGGAAGCAGAACTGACGGCACTGGATACTGCTACTGTTGAGGCAAAATGGTTG

Reverse complement sequence

CAACCATTTTGCCTCAACAGTAGCAGTATCCAGTGCCGTCAGTTCTGCTTCCATGGTTGACCTCGTCAAAATGGTCTGTTTGCAAGACCTCCACGAAACA[A/G]
CACCACCATCCAGTGTGAAGACATATCCACTAGTGGCTTTGATCTCATCCACATCAGAGATCCAGTTAGAATCACTATAACCCTCCAGTACTGCAGGATA

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	68.00%	2.90%	28.95%	0.06%	NA
All Indica	2759	60.30%	4.40%	35.23%	0.00%	NA
All Japonica	1512	92.70%	0.20%	7.08%	0.00%	NA
Aus	269	26.00%	3.70%	70.26%	0.00%	NA
Indica I	595	49.60%	4.40%	46.05%	0.00%	NA
Indica II	465	56.10%	6.20%	37.63%	0.00%	NA
Indica III	913	71.20%	3.40%	25.41%	0.00%	NA
Indica Intermediate	786	58.40%	4.60%	37.02%	0.00%	NA
Temperate Japonica	767	97.90%	0.10%	1.96%	0.00%	NA
Tropical Japonica	504	84.50%	0.00%	15.48%	0.00%	NA
Japonica Intermediate	241	93.40%	0.80%	5.81%	0.00%	NA
VI/Aromatic	96	31.20%	0.00%	65.62%	3.12%	NA
Intermediate	90	54.40%	4.40%	41.11%	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
vg0613848822	T -> C	LOC_Os06g23684.1	downstream_gene_variant ; 4741.0bp to feature; MODIFIER	silent_mutation	Average:23.805; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0613848822	T -> C	LOC_Os06g23684-LOC_Os06g23710	intergenic_region ; MODIFIER	silent_mutation	Average:23.805; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0613848822	T -> DEL	N	N	silent_mutation	Average:23.805; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613848822	NA	1.76E-08	mr1030_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
vg0613848822	4.48E-06	NA	mr1050_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
vg0613848822	9.38E-06	2.03E-06	mr1952_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 3 of 3 entries

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Search for Variation information by Variation ID:

Detailed information for vg0613848822:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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