RiceVarMap2

Detailed information for vg1223453994:

Variant ID: vg1223453994 (JBrowse)

Variation Type: SNP

Chromosome: chr12

Position: 23453994

Reference Allele: G

Alternative Allele: A

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATGCGCTGGTCCTCGAACCAGCAAACCCGTAGCAATCTCTCACGCTGCGACTTCCATTGGTGCTAGAGATATAATTCTACGCGCTGGTCCTCGAACCA[G/A]
TAAACCCGTAGCAATCTCTCACACCGCGACTTCCATTGGTGCTCGAGAGATAATTCTACGCGCTGGTTCTCGAACCAGTAAACCCGTAGCAATCTCCCAC

Reverse complement sequence

GTGGGAGATTGCTACGGGTTTACTGGTTCGAGAACCAGCGCGTAGAATTATCTCTCGAGCACCAATGGAAGTCGCGGTGTGAGAGATTGCTACGGGTTTA[C/T]
TGGTTCGAGGACCAGCGCGTAGAATTATATCTCTAGCACCAATGGAAGTCGCAGCGTGAGAGATTGCTACGGGTTTGCTGGTTCGAGGACCAGCGCATAG

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	90.60%	4.30%	0.91%	4.13%	NA
All Indica	2759	90.90%	0.80%	1.45%	6.89%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.33%	NA
Aus	269	35.70%	63.60%	0.74%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	67.10%	0.00%	4.95%	27.96%	NA
Indica III	913	98.20%	0.50%	0.55%	0.66%	NA
Indica Intermediate	786	89.60%	2.00%	1.53%	6.87%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	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	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg1223453994	G -> DEL	LOC_Os12g38190.1	N	frameshift_variant	Average:34.668; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg1223453994	G -> A	LOC_Os12g38190.1	missense_variant ; p.Ser365Asn; MODERATE	nonsynonymous_codon ; S365N	Average:34.668; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	unknown	unknown	DELETERIOUS	0.00

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223453994	NA	6.44E-12	mr1348	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
vg1223453994	NA	1.67E-06	mr1349	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 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg1223453994:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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