RiceVarMap2

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Detailed information for vg0724292753:

Variant ID: vg0724292753 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24292753
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.29, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ACATGAATTAGATCTTTTACATGGTTGCTTGTGTTCCTACAAGCTAGGCAGGGCATGGCTTGCAATAGACCAATAGACAATAGTTGATTCAGGTTTAAGA[C/T]
TTGCAATTTCAGTGGTAACTGAAGGTTGTTGAATCCCATCAGAAGTACAAAAATATAATACGTTTTCTTTGTATCTTTTCCATTAACTGGTTGGATCATT

Reverse complement sequence

AATGATCCAACCAGTTAATGGAAAAGATACAAAGAAAACGTATTATATTTTTGTACTTCTGATGGGATTCAACAACCTTCAGTTACCACTGAAATTGCAA[G/A]
TCTTAAACCTGAATCAACTATTGTCTATTGGTCTATTGCAAGCCATGCCCTGCCTAGCTTGTAGGAACACAAGCAACCATGTAAAAGATCTAATTCATGT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.10%	42.40%	0.04%	0.49%	NA
All Indica	2759	32.10%	67.20%	0.04%	0.65%	NA
All Japonica	1512	98.70%	1.10%	0.00%	0.13%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	85.50%	14.10%	0.00%	0.34%	NA
Indica II	465	22.20%	77.20%	0.00%	0.65%	NA
Indica III	913	3.00%	96.50%	0.00%	0.55%	NA
Indica Intermediate	786	31.30%	67.60%	0.13%	1.02%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.00%	0.83%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	57.80%	37.80%	1.11%	3.33%	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
vg0724292753	C -> DEL	N	N	silent_mutation	Average:67.346; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292753	C -> T	LOC_Os07g40550.1	3_prime_UTR_variant ; 596.0bp to feature; MODIFIER	silent_mutation	Average:67.346; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292753	C -> T	LOC_Os07g40550.2	3_prime_UTR_variant ; 596.0bp to feature; MODIFIER	silent_mutation	Average:67.346; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292753	C -> T	LOC_Os07g40550.3	3_prime_UTR_variant ; 596.0bp to feature; MODIFIER	silent_mutation	Average:67.346; most accessible tissue: Callus, score: 92.881	N	N	N	N
vg0724292753	C -> T	LOC_Os07g40540.1	downstream_gene_variant ; 2078.0bp to feature; MODIFIER	silent_mutation	Average:67.346; most accessible tissue: Callus, score: 92.881	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
vg0724292753	NA	1.28E-07	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

Showing 1 to 1 of 1 entries

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Search for Variation information by Variation ID:

Detailed information for vg0724292753:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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