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Detailed information for vg0418083292:

Variant ID: vg0418083292 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18083292
Reference Allele: CAlternative Allele: G,T,A
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.03, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTACCTTGGCAACCATCCTGTCGATAAGGATTTCCTTGGTACCCGTTTGTGCAATTGCATATATAGCCTGGTCCATTGGAGGAATTGAAGCACTCGCT[C/G,T,A]
TTGTCACTTTTACACGCGTATAACGTGAGATTTTTTTGTGCTTCGTCACAGTTGTTCACAGTTCGGATAGCCCAATCCAGTAGCATTGGCGCCCGGCCGC

Reverse complement sequence

GCGGCCGGGCGCCAATGCTACTGGATTGGGCTATCCGAACTGTGAACAACTGTGACGAAGCACAAAAAAATCTCACGTTATACGCGTGTAAAAGTGACAA[G/C,A,T]
AGCGAGTGCTTCAATTCCTCCAATGGACCAGGCTATATATGCAATTGCACAAACGGGTACCAAGGAAATCCTTATCGACAGGATGGTTGCCAAGGTAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.30% 42.70% 1.21% 5.78% A: 0.02%
All Indica  2759 68.40% 21.00% 1.23% 9.35% A: 0.04%
All Japonica  1512 21.10% 77.10% 0.93% 0.93% NA
Aus  269 45.70% 53.20% 1.12% 0.00% NA
Indica I  595 60.50% 37.50% 0.50% 1.51% NA
Indica II  465 54.80% 39.40% 1.51% 4.30% NA
Indica III  913 78.20% 2.10% 0.77% 18.84% A: 0.11%
Indica Intermediate  786 70.90% 19.70% 2.16% 7.25% NA
Temperate Japonica  767 0.30% 99.20% 0.00% 0.52% NA
Tropical Japonica  504 49.60% 47.00% 1.79% 1.59% NA
Japonica Intermediate  241 27.80% 69.30% 2.07% 0.83% NA
VI/Aromatic  96 21.90% 77.10% 1.04% 0.00% NA
Intermediate  90 28.90% 64.40% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0418083292 C -> A LOC_Os04g30280.1 missense_variant ; p.Lys255Asn; MODERATE nonsynonymous_codon ; K255N Average:58.861; most accessible tissue: Callus, score: 74.85 benign -0.205 TOLERATED 1.00
vg0418083292 C -> DEL LOC_Os04g30280.1 N frameshift_variant Average:58.861; most accessible tissue: Callus, score: 74.85 N N N N
vg0418083292 C -> G LOC_Os04g30280.1 missense_variant ; p.Lys255Asn; MODERATE nonsynonymous_codon ; K255N Average:58.861; most accessible tissue: Callus, score: 74.85 benign -0.205 TOLERATED 1.00
vg0418083292 C -> T LOC_Os04g30280.1 synonymous_variant ; p.Lys255Lys; LOW N Average:58.861; most accessible tissue: Callus, score: 74.85 N N N N
vg0418083292 C -> T LOC_Os04g30290.1 upstream_gene_variant ; 3315.0bp to feature; MODIFIER N Average:58.861; most accessible tissue: Callus, score: 74.85 N N N N
vg0418083292 C -> T LOC_Os04g30300.1 downstream_gene_variant ; 4619.0bp to feature; MODIFIER N Average:58.861; most accessible tissue: Callus, score: 74.85 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418083292 1.85E-08 NA mr1076 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
vg0418083292 NA 5.42E-06 mr1076 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
vg0418083292 8.35E-08 NA mr1082 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
vg0418083292 NA 4.05E-07 mr1082 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
vg0418083292 1.30E-06 NA mr1083 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
vg0418083292 NA 1.44E-06 mr1083 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
vg0418083292 1.67E-08 NA mr1104 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
vg0418083292 9.59E-06 NA mr1104 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
vg0418083292 1.29E-07 NA mr1107 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
vg0418083292 NA 2.13E-07 mr1220 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
vg0418083292 2.82E-11 NA mr1226 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
vg0418083292 2.59E-06 3.42E-07 mr1226 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
vg0418083292 NA 1.96E-06 mr1408 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
vg0418083292 1.43E-07 NA mr1411 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
vg0418083292 2.80E-06 NA mr1082_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
vg0418083292 5.88E-08 NA mr1104_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
vg0418083292 4.42E-07 NA mr1107_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
vg0418083292 2.38E-07 NA mr1226_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
vg0418083292 NA 3.55E-06 mr1870_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