RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0724293542:

Variant ID: vg0724293542 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24293542
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TCACTTTGTCATCCTAGAACTAGAATGGTTCCAAAACGGTTGATAGGTACTCCCTCCGTTTCACAATGTAAGTCATTCTAGCATTTCCCACATTCATATT[A/G]
ATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCGATATGAATGTGAGAAATGCTAGAATGACTTACATTGTGAAACGGAGGAAGTA

Reverse complement sequence

TACTTCCTCCGTTTCACAATGTAAGTCATTCTAGCATTTCTCACATTCATATCGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACAT[T/C]
AATATGAATGTGGGAAATGCTAGAATGACTTACATTGTGAAACGGAGGGAGTACCTATCAACCGTTTTGGAACCATTCTAGTTCTAGGATGACAAAGTGA

Allele Frequencies:

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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	57.00%	42.50%	0.25%	0.23%	NA
All Indica	2759	32.20%	67.20%	0.29%	0.36%	NA
All Japonica	1512	98.70%	1.20%	0.13%	0.00%	NA
Aus	269	82.90%	17.10%	0.00%	0.00%	NA
Indica I	595	85.40%	14.30%	0.00%	0.34%	NA
Indica II	465	22.80%	76.80%	0.00%	0.43%	NA
Indica III	913	3.00%	96.50%	0.22%	0.33%	NA
Indica Intermediate	786	31.40%	67.40%	0.76%	0.38%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	4.10%	0.83%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	56.70%	40.00%	2.22%	1.11%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

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Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724293542	A -> DEL	N	N	silent_mutation	Average:44.958; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293542	A -> G	LOC_Os07g40540.1	downstream_gene_variant ; 2867.0bp to feature; MODIFIER	silent_mutation	Average:44.958; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293542	A -> G	LOC_Os07g40550.1	intron_variant ; MODIFIER	silent_mutation	Average:44.958; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293542	A -> G	LOC_Os07g40550.2	intron_variant ; MODIFIER	silent_mutation	Average:44.958; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293542	A -> G	LOC_Os07g40550.3	intron_variant ; MODIFIER	silent_mutation	Average:44.958; most accessible tissue: Callus, score: 81.73	N	N	N	N

Showing 1 to 5 of 5 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724293542	NA	4.60E-08	mr1170_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
vg0724293542	NA	4.63E-06	mr1699_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 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0724293542:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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