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Detailed information for vg0614992514:

Variant ID: vg0614992514 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14992514
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGCAACCTCAGTGATGAAAGTGCTGAGAAAGCAGCTGGAAGAGATTCCGGCAGATGTCCATGGGTTAGATGTAGATGATGGTGTGAGTGAGCATGAGGC[T/C]
GATGTTGGCGATGGAGCTGGGCCATCGATCCATCGGGGTGGAAGTGTTGGTGATGAAATTAGCAGGCGTCCACCGCCAAAGTCAATGACAAAAGGGAGGG

Reverse complement sequence

CCCTCCCTTTTGTCATTGACTTTGGCGGTGGACGCCTGCTAATTTCATCACCAACACTTCCACCCCGATGGATCGATGGCCCAGCTCCATCGCCAACATC[A/G]
GCCTCATGCTCACTCACACCATCATCTACATCTAACCCATGGACATCTGCCGGAATCTCTTCCAGCTGCTTTCTCAGCACTTTCATCACTGAGGTTGCCC

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 52.90% 36.20% 0.78% 10.07% NA
All Indica  2759 81.40% 3.70% 0.83% 14.03% NA
All Japonica  1512 7.90% 90.90% 0.07% 1.12% NA
Aus  269 29.70% 69.90% 0.00% 0.37% NA
Indica I  595 93.10% 5.00% 0.17% 1.68% NA
Indica II  465 86.90% 1.90% 1.51% 9.68% NA
Indica III  913 73.10% 1.30% 0.88% 24.75% NA
Indica Intermediate  786 79.10% 6.50% 0.89% 13.49% NA
Temperate Japonica  767 2.10% 96.30% 0.13% 1.43% NA
Tropical Japonica  504 17.10% 82.30% 0.00% 0.60% NA
Japonica Intermediate  241 7.10% 91.70% 0.00% 1.24% NA
VI/Aromatic  96 17.70% 9.40% 10.42% 62.50% NA
Intermediate  90 42.20% 42.20% 3.33% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614992514 T -> C LOC_Os06g25660.1 synonymous_variant ; p.Ala398Ala; LOW synonymous_codon Average:28.084; most accessible tissue: Zhenshan97 flag leaf, score: 71.63 N N N N
vg0614992514 T -> DEL LOC_Os06g25660.1 N frameshift_variant Average:28.084; most accessible tissue: Zhenshan97 flag leaf, score: 71.63 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614992514 9.99E-06 3.03E-07 mr1020 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
vg0614992514 3.22E-08 3.22E-08 mr1032 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
vg0614992514 4.76E-07 4.76E-07 mr1165 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
vg0614992514 NA 1.69E-06 mr1395 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
vg0614992514 1.11E-08 1.11E-08 mr1478 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
vg0614992514 3.16E-07 3.16E-07 mr1536 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
vg0614992514 5.74E-06 9.70E-09 mr1971 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
vg0614992514 3.30E-07 5.01E-10 mr1165_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
vg0614992514 5.72E-07 1.38E-10 mr1548_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
vg0614992514 NA 3.60E-12 mr1728_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