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Detailed information for vg1204426116:

Variant ID: vg1204426116 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4426116
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGGTATTACGTTTCCTTGTATATCACGGAACGGCCTAAAGTCCTGGTTTGATAAGATTGTAAAGTAGATTTAGGAAACCGATACCGTATTGGATAAGG[A/T]
TTCTATCTTGTAATCCTGCCCCCCCTCCTATATAAGGTGGGCAGGAGGCCCTCTAGGGGGCATGACACAACCTGATCGTCAGATCAATACTACACCCGGC

Reverse complement sequence

GCCGGGTGTAGTATTGATCTGACGATCAGGTTGTGTCATGCCCCCTAGAGGGCCTCCTGCCCACCTTATATAGGAGGGGGGGCAGGATTACAAGATAGAA[T/A]
CCTTATCCAATACGGTATCGGTTTCCTAAATCTACTTTACAATCTTATCAAACCAGGACTTTAGGCCGTTCCGTGATATACAAGGAAACGTAATACCCAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 21.20% 1.10% 5.50% 72.15% NA
All Indica  2759 2.90% 1.00% 5.62% 90.43% NA
All Japonica  1512 55.30% 0.10% 0.53% 44.11% NA
Aus  269 14.90% 5.60% 26.02% 53.53% NA
Indica I  595 2.70% 0.30% 1.68% 95.29% NA
Indica II  465 3.40% 1.10% 8.60% 86.88% NA
Indica III  913 1.50% 0.50% 6.13% 91.79% NA
Indica Intermediate  786 4.50% 2.00% 6.23% 87.28% NA
Temperate Japonica  767 74.30% 0.00% 0.13% 25.55% NA
Tropical Japonica  504 40.50% 0.20% 0.99% 58.33% NA
Japonica Intermediate  241 25.70% 0.00% 0.83% 73.44% NA
VI/Aromatic  96 14.60% 8.30% 20.83% 56.25% NA
Intermediate  90 35.60% 1.10% 7.78% 55.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1204426116 A -> DEL N N silent_mutation Average:15.411; most accessible tissue: Minghui63 root, score: 29.362 N N N N
vg1204426116 A -> T LOC_Os12g08700-LOC_Os12g08710 intergenic_region ; MODIFIER silent_mutation Average:15.411; most accessible tissue: Minghui63 root, score: 29.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204426116 8.22E-06 NA mr1117 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
vg1204426116 NA 4.41E-07 mr1190 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
vg1204426116 2.16E-08 NA mr1679 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
vg1204426116 3.06E-08 NA mr1693 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
vg1204426116 NA 5.44E-07 mr1693 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
vg1204426116 NA 7.79E-13 mr1496_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