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Detailed information for vg1214107710:

Variant ID: vg1214107710 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14107710
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCTCCATGGTCGCGCCATGCCGTTGACCGCTCCGGCCGCCGGTGATGCCGCACCACGCCGCGCCGACCTCGCCCCACCGCGGCTTTGAGGCTGCTATGC[C/T]
GTCTCGGCGAAATCAACAAGAAGGGGAAAAGAAGGAACGAGTTGGAGAAAAGGAAGAAAAGAGAAGTGCAATCTGGGTATTTAGAAAAATATCTCACCTC

Reverse complement sequence

GAGGTGAGATATTTTTCTAAATACCCAGATTGCACTTCTCTTTTCTTCCTTTTCTCCAACTCGTTCCTTCTTTTCCCCTTCTTGTTGATTTCGCCGAGAC[G/A]
GCATAGCAGCCTCAAAGCCGCGGTGGGGCGAGGTCGGCGCGGCGTGGTGCGGCATCACCGGCGGCCGGAGCGGTCAACGGCATGGCGCGACCATGGAGGC

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 97.20% 1.70% 1.06% 0.00% NA
All Indica  2759 99.60% 0.10% 0.29% 0.00% NA
All Japonica  1512 92.20% 5.10% 2.71% 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 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 0.30% 0.76% 0.00% NA
Temperate Japonica  767 91.10% 3.90% 4.95% 0.00% NA
Tropical Japonica  504 90.50% 9.30% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 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
vg1214107710 C -> T LOC_Os12g24640.1 upstream_gene_variant ; 93.0bp to feature; MODIFIER silent_mutation Average:67.349; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg1214107710 C -> T LOC_Os12g24650.1 upstream_gene_variant ; 1578.0bp to feature; MODIFIER silent_mutation Average:67.349; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg1214107710 C -> T LOC_Os12g24640-LOC_Os12g24650 intergenic_region ; MODIFIER silent_mutation Average:67.349; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214107710 9.33E-06 9.33E-06 mr1108_2 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
vg1214107710 NA 2.71E-06 mr1148_2 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
vg1214107710 NA 3.83E-06 mr1200_2 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
vg1214107710 NA 1.83E-06 mr1204_2 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
vg1214107710 NA 3.49E-06 mr1252_2 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
vg1214107710 NA 8.27E-06 mr1318_2 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
vg1214107710 NA 1.55E-06 mr1358_2 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
vg1214107710 NA 2.21E-06 mr1405_2 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
vg1214107710 5.07E-06 5.07E-06 mr1421_2 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
vg1214107710 7.84E-07 7.84E-07 mr1455_2 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
vg1214107710 NA 5.58E-06 mr1741_2 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