RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0223953389:

Variant ID: vg0223953389 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23953389
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: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCAAGTCCTCAACCTGAGTAACAATATTTTGGACGGGATCATTCCGGACACGCTTACAAACTGTTCCAGTTTGACGCAGCTAGATTTGAGCATAAACT[T/C]
ATTTCAAGGCCAGATTCCCCTCGGCATAGGACTCCTCTCTGAGCTGTCGGATCTCGTGCTTTCTCGTAATTATCTCTCGGGGCACATTCCTTCTGAGCTC

Reverse complement sequence

GAGCTCAGAAGGAATGTGCCCCGAGAGATAATTACGAGAAAGCACGAGATCCGACAGCTCAGAGAGGAGTCCTATGCCGAGGGGAATCTGGCCTTGAAAT[A/G]
AGTTTATGCTCAAATCTAGCTGCGTCAAACTGGAACAGTTTGTAAGCGTGTCCGGAATGATCCCGTCCAAAATATTGTTACTCAGGTTGAGGACTTGCAA

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	68.10%	15.00%	0.32%	16.61%	NA
All Indica	2759	60.60%	14.00%	0.51%	24.86%	NA
All Japonica	1512	94.00%	4.40%	0.00%	1.59%	NA
Aus	269	14.50%	66.20%	0.37%	18.96%	NA
Indica I	595	84.20%	0.50%	0.00%	15.29%	NA
Indica II	465	68.20%	21.10%	0.65%	10.11%	NA
Indica III	913	42.60%	17.10%	0.66%	39.65%	NA
Indica Intermediate	786	59.30%	16.40%	0.64%	23.66%	NA
Temperate Japonica	767	93.00%	6.10%	0.00%	0.91%	NA
Tropical Japonica	504	95.20%	2.20%	0.00%	2.58%	NA
Japonica Intermediate	241	95.00%	3.30%	0.00%	1.66%	NA
VI/Aromatic	96	12.50%	67.70%	0.00%	19.79%	NA
Intermediate	90	80.00%	14.40%	0.00%	5.56%	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
vg0223953389	T -> DEL	LOC_Os02g39660.1	N	frameshift_variant	Average:60.072; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0223953389	T -> C	LOC_Os02g39660.1	missense_variant ; p.Leu155Ser; MODERATE	nonsynonymous_codon ; L155S	Average:60.072; most accessible tissue: Minghui63 panicle, score: 73.225	benign	0.347	TOLERATED	0.75

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223953389	NA	8.95E-06	mr1334	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
vg0223953389	NA	3.62E-07	mr1861	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
vg0223953389	NA	1.82E-08	mr1072_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
vg0223953389	NA	3.77E-08	mr1075_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 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0223953389:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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