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Detailed information for vg0135335946:

Variant ID: vg0135335946 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35335946
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACGGCAGCGCCGGTTTTCTCTAGCCTCCGCCCTCTTTCGACCAGTCCAGAAGCGCGATGGTTCGGCCCATATGCGGTCAAAGCGAAGGGGAAAAACCA[C/T]
GCATGGAAAGAAAACGAAGCCGCCCCTAGTCGGCCATGGCCATTGGCTACTTGCTGCCGTTCGTCGATCATCGCCTCCCACTACGCGGGTACAGGTCAAG

Reverse complement sequence

CTTGACCTGTACCCGCGTAGTGGGAGGCGATGATCGACGAACGGCAGCAAGTAGCCAATGGCCATGGCCGACTAGGGGCGGCTTCGTTTTCTTTCCATGC[G/A]
TGGTTTTTCCCCTTCGCTTTGACCGCATATGGGCCGAACCATCGCGCTTCTGGACTGGTCGAAAGAGGGCGGAGGCTAGAGAAAACCGGCGCTGCCGTCA

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 90.40% 9.60% 0.02% 0.00% NA
All Indica  2759 92.40% 7.60% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 13.40% 86.60% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 86.40% 13.60% 0.00% 0.00% NA
Indica Intermediate  786 91.60% 8.30% 0.13% 0.00% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0135335946 C -> T LOC_Os01g61060.1 downstream_gene_variant ; 4724.0bp to feature; MODIFIER silent_mutation Average:40.463; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0135335946 C -> T LOC_Os01g61070.1 downstream_gene_variant ; 2442.0bp to feature; MODIFIER silent_mutation Average:40.463; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N
vg0135335946 C -> T LOC_Os01g61070-LOC_Os01g61080 intergenic_region ; MODIFIER silent_mutation Average:40.463; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135335946 NA 5.18E-10 mr1499 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
vg0135335946 NA 5.78E-22 mr1817 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
vg0135335946 NA 6.36E-16 mr1897 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
vg0135335946 NA 7.39E-10 mr1939 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