RiceVarMap2

Detailed information for vg0408160817:

Variant ID: vg0408160817 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 8160817

Reference Allele: T

Alternative Allele: C

Primary Allele: T

Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, C: 0.47, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGACGGTACCTTGATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCT[T/C]
CTTTGGTTCCGGATGAAGGTCACCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCAACTTTCCATATACACCTAGGAAGCCA

Reverse complement sequence

TGGCTTCCTAGGTGTATATGGAAAGTTGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGTGACCTTCATCCGGAACCAAAG[A/G]
AGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATCAAGGTACCGTCTGG

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	34.50%	3.40%	36.39%	25.77%	NA
All Indica	2759	21.30%	5.50%	53.03%	20.19%	NA
All Japonica	1512	63.60%	0.20%	0.99%	35.25%	NA
Aus	269	14.90%	0.00%	69.89%	15.24%	NA
Indica I	595	29.40%	0.00%	47.90%	22.69%	NA
Indica II	465	26.90%	21.70%	34.62%	16.77%	NA
Indica III	913	15.40%	3.00%	61.99%	19.61%	NA
Indica Intermediate	786	18.60%	3.10%	57.38%	20.99%	NA
Temperate Japonica	767	96.10%	0.10%	0.39%	3.39%	NA
Tropical Japonica	504	11.10%	0.20%	1.59%	87.10%	NA
Japonica Intermediate	241	69.70%	0.40%	1.66%	28.22%	NA
VI/Aromatic	96	8.30%	0.00%	20.83%	70.83%	NA
Intermediate	90	36.70%	4.40%	37.78%	21.11%	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
vg0408160817	T -> C	LOC_Os04g14560.1	missense_variant ; p.Lys686Glu; MODERATE	nonsynonymous_codon ; K686E	Average:7.782; most accessible tissue: Minghui63 panicle, score: 20.733	benign	-0.712	TOLERATED	1.00
vg0408160817	T -> DEL	LOC_Os04g14560.1	N	frameshift_variant	Average:7.782; most accessible tissue: Minghui63 panicle, score: 20.733	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
vg0408160817	1.56E-06	7.88E-07	mr1167_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
vg0408160817	1.70E-06	1.70E-06	mr1574_2	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

Showing 1 to 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0408160817:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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