RiceVarMap2

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Detailed information for vg0724293541:

Variant ID: vg0724293541 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24293541
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.39, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTCACTTTGTCATCCTAGAACTAGAATGGTTCCAAAACGGTTGATAGGTACTCCCTCCGTTTCACAATGTAAGTCATTCTAGCATTTCCCACATTCATAT[T/C]
AATGTTAATGAATCTAGACATATATATCTATCTAGATTCATTAACATCGATATGAATGTGAGAAATGCTAGAATGACTTACATTGTGAAACGGAGGAAGT

Reverse complement sequence

ACTTCCTCCGTTTCACAATGTAAGTCATTCTAGCATTTCTCACATTCATATCGATGTTAATGAATCTAGATAGATATATATGTCTAGATTCATTAACATT[A/G]
ATATGAATGTGGGAAATGCTAGAATGACTTACATTGTGAAACGGAGGGAGTACCTATCAACCGTTTTGGAACCATTCTAGTTCTAGGATGACAAAGTGAA

Allele Frequencies:

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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	57.80%	41.70%	0.28%	0.19%	NA
All Indica	2759	32.30%	67.10%	0.33%	0.29%	NA
All Japonica	1512	98.70%	1.10%	0.13%	0.00%	NA
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	85.40%	14.30%	0.00%	0.34%	NA
Indica II	465	23.00%	76.60%	0.00%	0.43%	NA
Indica III	913	3.00%	96.60%	0.22%	0.22%	NA
Indica Intermediate	786	31.80%	67.00%	0.89%	0.25%	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	95.40%	3.70%	0.83%	0.00%	NA
VI/Aromatic	96	49.00%	51.00%	0.00%	0.00%	NA
Intermediate	90	62.20%	34.40%	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
vg0724293541	T -> DEL	N	N	silent_mutation	Average:44.9; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293541	T -> C	LOC_Os07g40540.1	downstream_gene_variant ; 2866.0bp to feature; MODIFIER	silent_mutation	Average:44.9; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293541	T -> C	LOC_Os07g40550.1	intron_variant ; MODIFIER	silent_mutation	Average:44.9; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293541	T -> C	LOC_Os07g40550.2	intron_variant ; MODIFIER	silent_mutation	Average:44.9; most accessible tissue: Callus, score: 81.73	N	N	N	N
vg0724293541	T -> C	LOC_Os07g40550.3	intron_variant ; MODIFIER	silent_mutation	Average:44.9; 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
vg0724293541	NA	4.02E-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
vg0724293541	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 vg0724293541:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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