\

Search for Variation information by Variation ID:

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

Detailed information for vg0124882911:

Variant ID: vg0124882911 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24882911
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGTGTGAAATCAATATTCAATATTAAAAACAGAAAAAAAAGAAAAAAAATCTTTAGTCCCGGTTGGTGTGCAACCGGGACTAAAGATCGATTTGAACC[A/G]
GGACTAAAGATAGCTTCGTAGTCCCGGTTGGAAAACCGGGACTACAGGGGGGTTACGAACCGGAACTAAAAAGCACTTCTCCACCAGTGATTGGTTCCTT

Reverse complement sequence

AAGGAACCAATCACTGGTGGAGAAGTGCTTTTTAGTTCCGGTTCGTAACCCCCCTGTAGTCCCGGTTTTCCAACCGGGACTACGAAGCTATCTTTAGTCC[T/C]
GGTTCAAATCGATCTTTAGTCCCGGTTGCACACCAACCGGGACTAAAGATTTTTTTTCTTTTTTTTCTGTTTTTAATATTGAATATTGATTTCACACCAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.40% 16.80% 4.10% 35.67% NA
All Indica  2759 55.30% 0.30% 2.72% 41.68% NA
All Japonica  1512 27.60% 50.40% 6.35% 15.67% NA
Aus  269 3.70% 0.40% 4.46% 91.45% NA
Indica I  595 35.60% 0.30% 0.67% 63.36% NA
Indica II  465 53.10% 0.60% 3.66% 42.58% NA
Indica III  913 64.40% 0.00% 4.16% 31.43% NA
Indica Intermediate  786 60.80% 0.50% 2.04% 36.64% NA
Temperate Japonica  767 15.50% 81.50% 2.35% 0.65% NA
Tropical Japonica  504 33.30% 11.50% 13.69% 41.47% NA
Japonica Intermediate  241 53.90% 32.80% 3.73% 9.54% NA
VI/Aromatic  96 72.90% 4.20% 1.04% 21.88% NA
Intermediate  90 33.30% 20.00% 11.11% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124882911 A -> G LOC_Os01g43460-LOC_Os01g43470 intergenic_region ; MODIFIER silent_mutation Average:47.861; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0124882911 A -> DEL N N silent_mutation Average:47.861; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124882911 4.16E-06 7.32E-06 mr1543 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
vg0124882911 NA 6.26E-09 mr1543 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
vg0124882911 NA 2.02E-16 mr1013_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
vg0124882911 NA 3.11E-15 mr1031_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
vg0124882911 NA 4.97E-06 mr1077_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
vg0124882911 NA 7.79E-06 mr1091_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
vg0124882911 NA 1.44E-07 mr1502_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
vg0124882911 1.31E-07 3.26E-09 mr1543_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
vg0124882911 NA 2.08E-12 mr1543_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
vg0124882911 NA 4.22E-07 mr1680_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
vg0124882911 NA 5.69E-09 mr1742_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
vg0124882911 NA 5.52E-06 mr1892_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