Search for Variation information by Variation ID:

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

Detailed information for vg0125479255:

Variant ID: vg0125479255 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25479255
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


ATATCTGCGCCAACTTTAGCGCCTCTCGAGATACCAGCTCCAGCACCTATGCCATCTTTTGCATTTGCATTCGCGTCAGCACCACCTCCAGCCTTCGCTC[T/C]
GATATCAGCGCCAACTTTAGCGCCTCCCGAGATACCAGCTCCAGCACCTATGCCATCTTTTGCATTTGCATTCGCGTCAGCACCAACTCCAGCCTTCGCT

Reverse complement sequence

AGCGAAGGCTGGAGTTGGTGCTGACGCGAATGCAAATGCAAAAGATGGCATAGGTGCTGGAGCTGGTATCTCGGGAGGCGCTAAAGTTGGCGCTGATATC[A/G]
GAGCGAAGGCTGGAGGTGGTGCTGACGCGAATGCAAATGCAAAAGATGGCATAGGTGCTGGAGCTGGTATCTCGAGAGGCGCTAAAGTTGGCGCAGATAT

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 48.20% 3.10% 17.01% 31.74% NA
All Indica  2759 29.70% 2.10% 23.78% 44.44% NA
All Japonica  1512 71.20% 5.60% 8.00% 15.15% NA
Aus  269 93.70% 0.00% 2.60% 3.72% NA
Indica I  595 26.90% 0.20% 38.49% 34.45% NA
Indica II  465 28.60% 0.00% 18.06% 53.33% NA
Indica III  913 32.00% 5.60% 17.42% 45.02% NA
Indica Intermediate  786 29.80% 0.80% 23.41% 46.06% NA
Temperate Japonica  767 75.70% 3.00% 9.00% 12.26% NA
Tropical Japonica  504 72.60% 6.90% 3.77% 16.67% NA
Japonica Intermediate  241 53.90% 11.20% 13.69% 21.16% NA
VI/Aromatic  96 80.20% 1.00% 4.17% 14.58% NA
Intermediate  90 57.80% 1.10% 17.78% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0125479255 T -> DEL LOC_Os01g44430.1 N frameshift_variant Average:39.343; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 N N N N
vg0125479255 T -> C LOC_Os01g44430.1 missense_variant ; p.Arg1135Gly; MODERATE nonsynonymous_codon ; R1135G Average:39.343; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 unknown unknown TOLERATED 0.76

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125479255 NA 5.55E-06 mr1219 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
vg0125479255 NA 3.65E-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
vg0125479255 NA 9.05E-07 mr1756 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
vg0125479255 NA 2.61E-10 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
vg0125479255 NA 1.11E-08 mr1946 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
vg0125479255 NA 8.94E-18 mr1131_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
vg0125479255 2.43E-06 1.86E-07 mr1219_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
vg0125479255 NA 3.13E-15 mr1744_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