Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0105180474:

Variant ID: vg0105180474 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5180474
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGAATGCCAGTGTTCAACGCTCCTGCGTTGACAGCACTTGTGGACAGATGGAGGCCTGAGACACATAGCTTCCACCTCCCCAGTGGTGAGATGACTAT[C/T]
ACTCTACAGGATGTGGCTATGATCTTGGCCCTCCCATTACGGGGGCATGCCGTGACGGGCAGGACAGAGACTCCTGGATGGCGTGCACAAGTGGAGCAGC

Reverse complement sequence

GCTGCTCCACTTGTGCACGCCATCCAGGAGTCTCTGTCCTGCCCGTCACGGCATGCCCCCGTAATGGGAGGGCCAAGATCATAGCCACATCCTGTAGAGT[G/A]
ATAGTCATCTCACCACTGGGGAGGTGGAAGCTATGTGTCTCAGGCCTCCATCTGTCCACAAGTGCTGTCAACGCAGGAGCGTTGAACACTGGCATTCCTC

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 50.70% 48.90% 0.42% 0.00% NA
All Indica  2759 20.80% 78.50% 0.65% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 66.90% 32.70% 0.37% 0.00% NA
Indica I  595 53.60% 45.40% 1.01% 0.00% NA
Indica II  465 3.00% 96.10% 0.86% 0.00% NA
Indica III  913 3.10% 96.70% 0.22% 0.00% NA
Indica Intermediate  786 27.20% 72.00% 0.76% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 55.60% 43.30% 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
vg0105180474 C -> T LOC_Os01g09960.1 intron_variant ; MODIFIER silent_mutation Average:35.13; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105180474 NA 9.61E-06 mr1030 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
vg0105180474 NA 2.11E-06 mr1058 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
vg0105180474 NA 9.94E-14 mr1170 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
vg0105180474 NA 5.38E-06 mr1285 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
vg0105180474 NA 4.50E-11 mr1316 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
vg0105180474 NA 1.44E-06 mr1345 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
vg0105180474 NA 6.17E-06 mr1378 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
vg0105180474 NA 2.16E-09 mr1379 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
vg0105180474 NA 2.31E-06 mr1568 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
vg0105180474 NA 5.02E-06 mr1629 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
vg0105180474 NA 2.10E-09 mr1637 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
vg0105180474 NA 3.36E-13 mr1663 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
vg0105180474 NA 3.33E-11 mr1819 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
vg0105180474 NA 7.32E-06 mr1875 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
vg0105180474 4.60E-06 NA mr1895 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
vg0105180474 NA 9.02E-06 mr1908 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
vg0105180474 NA 2.42E-14 mr1982 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