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Detailed information for vg0109580082:

Variant ID: vg0109580082 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9580082
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGCCTCCTACTCTGTACTGCGCCGTCGCTCGTAGACTACTCCATCCCGCTCGCCGGCGTGCACCAGCGATCGGGAGAGCAGGTCTCCAGAACCTCTG[T/C]
CTTTGACGTCCTGCACCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTCGCGCGACTGCTCCCTGTTCGTTCGCGACGGCTCGCCTTCCTCTTCG

Reverse complement sequence

CGAAGAGGAAGGCGAGCCGTCGCGAACGAACAGGGAGCAGTCGCGCGAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGGTGCAGGACGTCAAAG[A/G]
CAGAGGTTCTGGAGACCTGCTCTCCCGATCGCTGGTGCACGCCGGCGAGCGGGATGGAGTAGTCTACGAGCGACGGCGCAGTACAGAGTAGGAGGCAAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.70% 0.10% 0.15% 65.00% NA
All Indica  2759 4.60% 0.20% 0.07% 95.18% NA
All Japonica  1512 96.90% 0.00% 0.00% 3.11% NA
Aus  269 1.10% 0.40% 0.74% 97.77% NA
Indica I  595 7.10% 0.20% 0.00% 92.77% NA
Indica II  465 1.70% 0.40% 0.00% 97.85% NA
Indica III  913 3.80% 0.20% 0.11% 95.84% NA
Indica Intermediate  786 5.20% 0.00% 0.13% 94.66% NA
Temperate Japonica  767 98.70% 0.00% 0.00% 1.30% NA
Tropical Japonica  504 94.60% 0.00% 0.00% 5.36% NA
Japonica Intermediate  241 95.90% 0.00% 0.00% 4.15% NA
VI/Aromatic  96 10.40% 0.00% 0.00% 89.58% NA
Intermediate  90 41.10% 0.00% 3.33% 55.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0109580082 T -> DEL N N silent_mutation Average:10.033; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0109580082 T -> C LOC_Os01g16820.1 downstream_gene_variant ; 1168.0bp to feature; MODIFIER silent_mutation Average:10.033; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0109580082 T -> C LOC_Os01g16820-LOC_Os01g16840 intergenic_region ; MODIFIER silent_mutation Average:10.033; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109580082 NA 1.63E-06 mr1184_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
vg0109580082 NA 2.97E-06 mr1289_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
vg0109580082 NA 8.82E-06 mr1329_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
vg0109580082 NA 3.74E-07 mr1488_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
vg0109580082 NA 2.61E-09 mr1506_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
vg0109580082 NA 3.80E-07 mr1524_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
vg0109580082 NA 3.21E-12 mr1636_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
vg0109580082 NA 2.99E-19 mr1682_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
vg0109580082 NA 1.02E-09 mr1683_2 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
vg0109580082 NA 3.70E-07 mr1824_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
vg0109580082 NA 3.18E-14 mr1838_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