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Detailed information for vg0433018887:

Variant ID: vg0433018887 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33018887
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.07, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTAATCACCTCAATCTCTTTCTTCTTTACCCTTCCCTCTCTCACTCCGCTGCAACACTGACAAAAAGCAATGCACAGGCGCCTAGGAGCTCGTGTGCG[C/T]
TAGCGACTAATTTACCATCCGCTCGCACCCTCTTTCCACCTTTCTCTCGTCCATGTCATCATCCAATCTGACGTGTAGCTCATATCGCCGGCTCAATCTA

Reverse complement sequence

TAGATTGAGCCGGCGATATGAGCTACACGTCAGATTGGATGATGACATGGACGAGAGAAAGGTGGAAAGAGGGTGCGAGCGGATGGTAAATTAGTCGCTA[G/A]
CGCACACGAGCTCCTAGGCGCCTGTGCATTGCTTTTTGTCAGTGTTGCAGCGGAGTGAGAGAGGGAAGGGTAAAGAAGAAAGAGATTGAGGTGATTAAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.00% 32.90% 0.06% 0.00% NA
All Indica  2759 97.70% 2.30% 0.04% 0.00% NA
All Japonica  1512 15.20% 84.70% 0.07% 0.00% NA
Aus  269 37.90% 62.10% 0.00% 0.00% NA
Indica I  595 94.60% 5.40% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 41.10% 58.90% 0.00% 0.00% NA
Japonica Intermediate  241 7.10% 92.50% 0.41% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 60.00% 38.90% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0433018887 C -> T LOC_Os04g55505.1 upstream_gene_variant ; 3392.0bp to feature; MODIFIER silent_mutation Average:53.279; most accessible tissue: Minghui63 root, score: 87.205 N N N N
vg0433018887 C -> T LOC_Os04g55510.1 upstream_gene_variant ; 3829.0bp to feature; MODIFIER silent_mutation Average:53.279; most accessible tissue: Minghui63 root, score: 87.205 N N N N
vg0433018887 C -> T LOC_Os04g55505-LOC_Os04g55510 intergenic_region ; MODIFIER silent_mutation Average:53.279; most accessible tissue: Minghui63 root, score: 87.205 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433018887 NA 1.90E-08 mr1040 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
vg0433018887 NA 4.10E-07 mr1925 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
vg0433018887 NA 8.30E-16 mr1040_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
vg0433018887 NA 1.57E-07 mr1097_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
vg0433018887 NA 1.81E-06 mr1243_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
vg0433018887 NA 3.95E-06 mr1252_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
vg0433018887 NA 6.61E-07 mr1295_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
vg0433018887 6.59E-06 1.14E-20 mr1362_2 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
vg0433018887 5.96E-07 2.59E-09 mr1498_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
vg0433018887 NA 6.05E-06 mr1567_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
vg0433018887 NA 6.03E-17 mr1746_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
vg0433018887 NA 1.46E-08 mr1800_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