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Detailed information for vg0420234496:

Variant ID: vg0420234496 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20234496
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGCTTGTGGCAAACTAGGGTCAAAGATTTGTTAGCTCAACAAGAAGTTTCAAAGGCTTTGAAGGGTGTCAAACCGGCCAAGATGGAGGATGACGATTG[T/G]
GAGGAGATGCAGTTGCAGGCGGCTGCGACAATAAGGCGATGTCTTTCAGATCAGATCATGTACCATGTGATGGAGGAGACCTCACCAAAGATAATTTGGG

Reverse complement sequence

CCCAAATTATCTTTGGTGAGGTCTCCTCCATCACATGGTACATGATCTGATCTGAAAGACATCGCCTTATTGTCGCAGCCGCCTGCAACTGCATCTCCTC[A/C]
CAATCGTCATCCTCCATCTTGGCCGGTTTGACACCCTTCAAAGCCTTTGAAACTTCTTGTTGAGCTAACAAATCTTTGACCCTAGTTTGCCACAAGCCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.80% 1.60% 3.11% 54.53% NA
All Indica  2759 9.20% 1.00% 4.39% 85.43% NA
All Japonica  1512 96.80% 2.70% 0.07% 0.46% NA
Aus  269 26.80% 1.10% 7.43% 64.68% NA
Indica I  595 4.00% 0.30% 1.18% 94.45% NA
Indica II  465 12.70% 1.10% 1.94% 84.30% NA
Indica III  913 8.40% 1.40% 8.32% 81.82% NA
Indica Intermediate  786 11.80% 1.00% 3.69% 83.46% NA
Temperate Japonica  767 94.50% 5.20% 0.00% 0.26% NA
Tropical Japonica  504 98.80% 0.00% 0.20% 0.99% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 0.00% 3.12% 19.79% NA
Intermediate  90 72.20% 3.30% 2.22% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0420234496 T -> DEL LOC_Os04g33410.1 N frameshift_variant Average:16.342; most accessible tissue: Callus, score: 55.513 N N N N
vg0420234496 T -> G LOC_Os04g33410.1 missense_variant ; p.Cys134Trp; MODERATE nonsynonymous_codon ; C134W Average:16.342; most accessible tissue: Callus, score: 55.513 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420234496 NA 1.36E-25 mr1632 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
vg0420234496 4.63E-06 NA mr1138_2 Ind_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
vg0420234496 NA 6.37E-13 mr1191_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
vg0420234496 NA 8.20E-11 mr1537_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
vg0420234496 NA 6.57E-29 mr1631_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
vg0420234496 NA 2.36E-17 mr1712_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
vg0420234496 NA 7.70E-07 mr1727_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
vg0420234496 NA 7.66E-13 mr1770_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
vg0420234496 NA 7.57E-09 mr1946_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
vg0420234496 8.81E-06 5.52E-06 mr1946_2 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
vg0420234496 NA 7.57E-09 mr1948_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
vg0420234496 8.81E-06 5.52E-06 mr1948_2 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