Search for Variation information by Variation ID:

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

Detailed information for vg0423007797:

Variant ID: vg0423007797 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 23007797
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAAATAAAAAAAATAAAACCCTCCTCTCCACACCGGTCCCCATGTCACGCCCCAAACTAGTCCCGACCGGAACTAGCCCGTGACGCTCCAAATTAACCT[A/G]
TTAATCGATACCAGTCCCAGAAAACAGTGCTGGTATCACAGGAAGACAGATTATCACAGCAACAGAGGTCTCTTTATTATAGAGTAGGAGTACAATCAAG

Reverse complement sequence

CTTGATTGTACTCCTACTCTATAATAAAGAGACCTCTGTTGCTGTGATAATCTGTCTTCCTGTGATACCAGCACTGTTTTCTGGGACTGGTATCGATTAA[T/C]
AGGTTAATTTGGAGCGTCACGGGCTAGTTCCGGTCGGGACTAGTTTGGGGCGTGACATGGGGACCGGTGTGGAGAGGAGGGTTTTATTTTTTTTATTTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.10% 2.90% 8.32% 1.65% NA
All Indica  2759 88.50% 0.40% 9.64% 1.52% NA
All Japonica  1512 93.30% 6.60% 0.07% 0.07% NA
Aus  269 41.60% 1.90% 44.98% 11.52% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 0.00% 1.94% 0.43% NA
Indica III  913 76.20% 0.90% 21.36% 1.53% NA
Indica Intermediate  786 88.50% 0.30% 7.89% 3.31% NA
Temperate Japonica  767 87.60% 12.30% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.00% 0.20% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 20.80% 2.08% 1.04% NA
Intermediate  90 91.10% 2.20% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0423007797 A -> DEL N N silent_mutation Average:51.002; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0423007797 A -> G LOC_Os04g38730.1 upstream_gene_variant ; 4255.0bp to feature; MODIFIER silent_mutation Average:51.002; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0423007797 A -> G LOC_Os04g38730-LOC_Os04g38740 intergenic_region ; MODIFIER silent_mutation Average:51.002; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0423007797 1.74E-07 NA mr1210 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
vg0423007797 NA 1.87E-08 mr1210 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
vg0423007797 NA 8.18E-07 mr1305 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
vg0423007797 NA 3.96E-09 mr1585 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
vg0423007797 6.72E-08 NA mr1586 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
vg0423007797 NA 1.08E-08 mr1586 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
vg0423007797 3.39E-07 NA mr1765 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
vg0423007797 NA 3.65E-07 mr1765 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
vg0423007797 NA 1.31E-06 mr1305_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
vg0423007797 NA 5.12E-08 mr1585_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
vg0423007797 NA 1.50E-06 mr1765_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