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Detailed information for vg0402405188:

Variant ID: vg0402405188 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2405188
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TTACAGAATCCGTCAGTAAACCGCGAGACGAATTTATTAAGCCTAGTTAAGCCGTTATTAGCAAATGTTTACTGTAGCACCACATTGTTAAATCATGGAG[C/T]
AATTAGGCTCAAAAGATTCGTCTCGCAAATTAGTCACAATCTGTCCAATTGGTTATTTTTTTAAGACTATATTTAATATTTTATGCAGGTGTTCGATATG

Reverse complement sequence

CATATCGAACACCTGCATAAAATATTAAATATAGTCTTAAAAAAATAACCAATTGGACAGATTGTGACTAATTTGCGAGACGAATCTTTTGAGCCTAATT[G/A]
CTCCATGATTTAACAATGTGGTGCTACAGTAAACATTTGCTAATAACGGCTTAACTAGGCTTAATAAATTCGTCTCGCGGTTTACTGACGGATTCTGTAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.40% 3.60% 2.54% 6.41% NA
All Indica  2759 99.50% 0.30% 0.22% 0.04% NA
All Japonica  1512 65.60% 8.00% 7.41% 18.98% NA
Aus  269 98.50% 0.40% 0.37% 0.74% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.20% 0.43% 0.22% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.30% 0.51% 0.00% NA
Temperate Japonica  767 57.80% 2.90% 13.30% 26.08% NA
Tropical Japonica  504 81.00% 6.00% 0.20% 12.90% NA
Japonica Intermediate  241 58.50% 28.60% 3.73% 9.13% NA
VI/Aromatic  96 49.00% 42.70% 1.04% 7.29% NA
Intermediate  90 92.20% 1.10% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402405188 C -> DEL N N silent_mutation Average:44.13; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0402405188 C -> T LOC_Os04g04970.1 upstream_gene_variant ; 2837.0bp to feature; MODIFIER silent_mutation Average:44.13; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0402405188 C -> T LOC_Os04g04950-LOC_Os04g04970 intergenic_region ; MODIFIER silent_mutation Average:44.13; 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
vg0402405188 NA 5.74E-07 mr1117 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
vg0402405188 NA 4.53E-06 mr1118 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
vg0402405188 NA 5.70E-06 mr1242 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
vg0402405188 NA 4.42E-06 mr1247 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
vg0402405188 NA 1.05E-06 mr1496 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
vg0402405188 NA 1.50E-06 mr1114_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
vg0402405188 NA 3.07E-08 mr1117_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
vg0402405188 NA 9.60E-08 mr1118_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
vg0402405188 NA 2.36E-07 mr1119_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
vg0402405188 NA 2.68E-06 mr1120_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
vg0402405188 NA 1.66E-07 mr1123_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
vg0402405188 1.33E-06 1.33E-06 mr1197_2 Jap_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
vg0402405188 NA 1.29E-08 mr1240_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
vg0402405188 NA 6.30E-07 mr1242_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
vg0402405188 NA 4.49E-07 mr1247_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
vg0402405188 NA 4.97E-09 mr1496_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