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Detailed information for vg0218321013:

Variant ID: vg0218321013 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18321013
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTGGTTTGAGTACGGATGGCATGAACCCTTTTGGAGAGATGAGCAGCGGCCATAGCACTTGGCCCATTACGATGTGTATCTACAACCTCCCCCCATG[G/C]
CTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATCGATGTGTACCTAAGACCACTGGTCGAAG

Reverse complement sequence

CTTCGACCAGTGGTCTTAGGTACACATCGATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAG[C/G]
CATGGGGGGAGGTTGTAGATACACATCGTAATGGGCCAAGTGCTATGGCCGCTGCTCATCTCTCCAAAAGGGTTCATGCCATCCGTACTCAAACCAAACC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 0.40% 0.74% 0.83% NA
All Indica  2759 96.70% 0.70% 1.27% 1.38% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.60% 0.30% 1.85% 2.18% NA
Indica II  465 97.20% 0.20% 1.72% 0.86% NA
Indica III  913 97.30% 1.20% 0.55% 0.99% NA
Indica Intermediate  786 96.60% 0.50% 1.40% 1.53% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0218321013 G -> C LOC_Os02g30740.1 missense_variant ; p.Trp178Cys; MODERATE N Average:11.693; most accessible tissue: Zhenshan97 flower, score: 14.863 N N N N
vg0218321013 G -> C LOC_Os02g30730.1 upstream_gene_variant ; 3716.0bp to feature; MODIFIER N Average:11.693; most accessible tissue: Zhenshan97 flower, score: 14.863 N N N N
vg0218321013 G -> C LOC_Os02g30750.1 upstream_gene_variant ; 3815.0bp to feature; MODIFIER N Average:11.693; most accessible tissue: Zhenshan97 flower, score: 14.863 N N N N
vg0218321013 G -> C LOC_Os02g30730.2 upstream_gene_variant ; 3716.0bp to feature; MODIFIER N Average:11.693; most accessible tissue: Zhenshan97 flower, score: 14.863 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218321013 NA 8.38E-06 mr1186 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
vg0218321013 NA 5.22E-07 mr1236 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
vg0218321013 NA 9.44E-07 mr1236 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
vg0218321013 NA 1.06E-06 mr1639 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
vg0218321013 5.71E-06 5.71E-06 mr1891 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