RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0323186777:

Variant ID: vg0323186777 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 23186777
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCAGCAAAACACCGACCCTGTGCCATGACATCTAGACTACCGAGCCGCAACTCGTGTAGCCTTCATTTGTCCTAGAGATGTCCATCGAGTCCCGACTTC[G/A]
TCCATCTCCATCCGTGTACCTTTGTTTATGACCAGACTGAGCCACAAACTACGCCTTACCCACTAGACATGTGGAAGTACGGTAGTGCTTTGCAACAGAG

Reverse complement sequence

CTCTGTTGCAAAGCACTACCGTACTTCCACATGTCTAGTGGGTAAGGCGTAGTTTGTGGCTCAGTCTGGTCATAAACAAAGGTACACGGATGGAGATGGA[C/T]
GAAGTCGGGACTCGATGGACATCTCTAGGACAAATGAAGGCTACACGAGTTGCGGCTCGGTAGTCTAGATGTCATGGCACAGGGTCGGTGTTTTGCTGCT

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	93.80%	5.40%	0.85%	0.00%	NA
All Indica	2759	97.70%	0.90%	1.38%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	17.10%	82.20%	0.74%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	97.70%	0.40%	1.86%	0.00%	NA
Indica Intermediate	786	94.80%	2.80%	2.42%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0323186777	G -> A	LOC_Os03g41750.1	upstream_gene_variant ; 2459.0bp to feature; MODIFIER	silent_mutation	Average:48.03; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	N	N	N	N
vg0323186777	G -> A	LOC_Os03g41740.1	intron_variant ; MODIFIER	silent_mutation	Average:48.03; most accessible tissue: Zhenshan97 flag leaf, score: 56.722	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
vg0323186777	6.14E-06	3.00E-06	mr1029	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
vg0323186777	5.51E-06	NA	mr1047	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
vg0323186777	NA	2.61E-07	mr1184	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
vg0323186777	NA	8.43E-06	mr1424	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
vg0323186777	6.12E-07	3.27E-13	mr1471	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
vg0323186777	NA	2.16E-18	mr1515	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
vg0323186777	2.28E-06	NA	mr1543	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
vg0323186777	NA	9.62E-06	mr1625	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
vg0323186777	NA	2.44E-08	mr1706	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
vg0323186777	NA	2.69E-11	mr1722	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 20 entries

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Search for Variation information by Variation ID:

Detailed information for vg0323186777:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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