RiceVarMap2

Detailed information for vg1220167325:

Variant ID: vg1220167325 (JBrowse)

Variation Type: SNP

Chromosome: chr12

Position: 20167325

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCGTCCGACTGGTTTCCAGTCGGGGGCTCTTGAGTTGTTGCCGTTTCAGTTGTTGCCGACTGGTTTCCAGTCGGCGGCAGGTCACTCGGATCGGCCCT[A/G]
TCGCCCGAAGCATGGGCACCAGTCGGCTGGCTTTCAGTGGTCGGCTGGTTTTCAACAGTCGGCTCGGGGTCCTTGGATATATTTTGCTCTGTCATGCCAG

Reverse complement sequence

CTGGCATGACAGAGCAAAATATATCCAAGGACCCCGAGCCGACTGTTGAAAACCAGCCGACCACTGAAAGCCAGCCGACTGGTGCCCATGCTTCGGGCGA[T/C]
AGGGCCGATCCGAGTGACCTGCCGCCGACTGGAAACCAGTCGGCAACAACTGAAACGGCAACAACTCAAGAGCCCCCGACTGGAAACCAGTCGGACGCAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.00%	6.70%	49.81%	19.49%	NA
All Indica	2759	3.70%	10.10%	69.74%	16.46%	NA
All Japonica	1512	64.30%	1.10%	14.09%	20.57%	NA
Aus	269	8.20%	7.10%	39.78%	44.98%	NA
Indica I	595	5.00%	13.30%	47.56%	34.12%	NA
Indica II	465	4.50%	8.60%	77.42%	9.46%	NA
Indica III	913	2.50%	8.40%	82.58%	6.46%	NA
Indica Intermediate	786	3.60%	10.60%	67.05%	18.83%	NA
Temperate Japonica	767	93.10%	0.00%	2.74%	4.17%	NA
Tropical Japonica	504	21.80%	2.80%	32.34%	43.06%	NA
Japonica Intermediate	241	61.40%	0.80%	12.03%	25.73%	NA
VI/Aromatic	96	5.20%	2.10%	67.71%	25.00%	NA
Intermediate	90	35.60%	2.20%	50.00%	12.22%	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
vg1220167325	A -> DEL	LOC_Os12g33340.1	N	frameshift_variant	Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N
vg1220167325	A -> G	LOC_Os12g33340.1	synonymous_variant ; p.Asp438Asp; LOW	synonymous_codon	Average:19.0; most accessible tissue: Minghui63 young leaf, score: 40.718	N	N	N	N

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
vg1220167325	4.07E-06	3.31E-07	mr1224	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
vg1220167325	NA	1.93E-08	mr1593	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 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg1220167325:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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