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Detailed information for vg0129870980:

Variant ID: vg0129870980 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29870980
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGAAATTTCAGCCACACTACTTAGGATTTCCACATAATCATATGGCAAAGAAAGACGCAACAACAACAGTTCCTAAGATCAAGCCTAGATCTATAATAC[C/T]
AGCATAGTATGGTGAAGAAGCATAGAAGCTGCATAAGAAACCAAAGATTATATTTAAAAGAGGCCTTCACACATGGGAGTTTAACGTCAGTTCAGCTTGA

Reverse complement sequence

TCAAGCTGAACTGACGTTAAACTCCCATGTGTGAAGGCCTCTTTTAAATATAATCTTTGGTTTCTTATGCAGCTTCTATGCTTCTTCACCATACTATGCT[G/A]
GTATTATAGATCTAGGCTTGATCTTAGGAACTGTTGTTGTTGCGTCTTTCTTTGCCATATGATTATGTGGAAATCCTAAGTAGTGTGGCTGAAATTTCGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 3.00% 1.12% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 87.20% 9.40% 3.44% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 76.00% 17.70% 6.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 2.50% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg0129870980 C -> T LOC_Os01g51960.1 upstream_gene_variant ; 1725.0bp to feature; MODIFIER silent_mutation Average:52.035; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N
vg0129870980 C -> T LOC_Os01g51970.1 upstream_gene_variant ; 184.0bp to feature; MODIFIER silent_mutation Average:52.035; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N
vg0129870980 C -> T LOC_Os01g51980.1 upstream_gene_variant ; 3506.0bp to feature; MODIFIER silent_mutation Average:52.035; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N
vg0129870980 C -> T LOC_Os01g51950.1 downstream_gene_variant ; 4556.0bp to feature; MODIFIER silent_mutation Average:52.035; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N
vg0129870980 C -> T LOC_Os01g51960-LOC_Os01g51970 intergenic_region ; MODIFIER silent_mutation Average:52.035; most accessible tissue: Zhenshan97 young leaf, score: 70.177 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129870980 NA 6.32E-06 mr1126 Jap_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
vg0129870980 3.75E-06 NA mr1677 Jap_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