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Detailed information for vg0700179866:

Variant ID: vg0700179866 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 179866
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CAACTGTTCCACATTTTGAACTTGGGATGAAGTTTAACTCCAAAGCTCAGTTCAGGGCAGCCATTACAAGATATGCCTTGAGTGAAAGGAAGGTGATCAA[C/T]
TTCATCAAAAGTGATCCAAAAAGAGTGAGGGCAAAATATGACTGGTCCAGCTGCCCTTGGGTATGTTTGTTGTCAAAGACTTCAAGGTCTGACAGTTGGC

Reverse complement sequence

GCCAACTGTCAGACCTTGAAGTCTTTGACAACAAACATACCCAAGGGCAGCTGGACCAGTCATATTTTGCCCTCACTCTTTTTGGATCACTTTTGATGAA[G/A]
TTGATCACCTTCCTTTCACTCAAGGCATATCTTGTAATGGCTGCCCTGAACTGAGCTTTGGAGTTAAACTTCATCCCAAGTTCAAAATGTGGAACAGTTG

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 56.00% 31.30% 1.25% 11.49% NA
All Indica  2759 80.00% 7.40% 1.20% 11.42% NA
All Japonica  1512 22.60% 76.40% 0.33% 0.73% NA
Aus  269 19.00% 0.00% 6.32% 74.72% NA
Indica I  595 97.60% 1.80% 0.00% 0.50% NA
Indica II  465 51.60% 27.30% 3.87% 17.20% NA
Indica III  913 81.90% 0.30% 0.22% 17.52% NA
Indica Intermediate  786 81.30% 7.90% 1.65% 9.16% NA
Temperate Japonica  767 23.60% 75.40% 0.13% 0.91% NA
Tropical Japonica  504 28.40% 70.40% 0.40% 0.79% NA
Japonica Intermediate  241 7.10% 92.10% 0.83% 0.00% NA
VI/Aromatic  96 7.30% 85.40% 1.04% 6.25% NA
Intermediate  90 43.30% 42.20% 3.33% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0700179866 C -> DEL LOC_Os07g01290.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0700179866 C -> T LOC_Os07g01290.1 synonymous_variant ; p.Asn289Asn; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0700179866 NA 1.64E-06 mr1158 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
vg0700179866 NA 2.78E-06 mr1352 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
vg0700179866 2.88E-06 8.11E-09 mr1383 Ind_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
vg0700179866 NA 4.04E-07 mr1835 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
vg0700179866 NA 6.15E-06 mr1042_2 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
vg0700179866 NA 8.52E-12 mr1158_2 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
vg0700179866 NA 4.76E-06 mr1168_2 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
vg0700179866 NA 1.19E-11 mr1383_2 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