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Detailed information for vg0402093212:

Variant ID: vg0402093212 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2093212
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTCCAGAAATATGTCATTCATTTGGATGGATGTCATCCTCTTTCCATGAGGAATCCTAGGAAGAGATGTGCTTGGTGCTCACTCCGTGATATTCGCG[T/C]
GGCTTGCGACGTGAATTTCAGAAGCAACGAAACAACCCGGGGCAACAGTAATAGTTGCGAACATGTGTCCAAGGAAAATATGTAGCCAATAGTGTGATGA

Reverse complement sequence

TCATCACACTATTGGCTACATATTTTCCTTGGACACATGTTCGCAACTATTACTGTTGCCCCGGGTTGTTTCGTTGCTTCTGAAATTCACGTCGCAAGCC[A/G]
CGCGAATATCACGGAGTGAGCACCAAGCACATCTCTTCCTAGGATTCCTCATGGAAAGAGGATGACATCCATCCAAATGAATGACATATTTCTGGAGGGA

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 14.80% 13.90% 0.32% 70.95% NA
All Indica  2759 2.00% 5.40% 0.29% 92.35% NA
All Japonica  1512 34.30% 32.90% 0.26% 32.61% NA
Aus  269 15.20% 1.10% 0.00% 83.64% NA
Indica I  595 0.20% 11.80% 0.34% 87.73% NA
Indica II  465 0.90% 7.10% 0.22% 91.83% NA
Indica III  913 2.50% 0.50% 0.22% 96.71% NA
Indica Intermediate  786 3.30% 5.20% 0.38% 91.09% NA
Temperate Japonica  767 35.20% 58.70% 0.13% 6.00% NA
Tropical Japonica  504 28.00% 2.60% 0.60% 68.85% NA
Japonica Intermediate  241 44.40% 14.10% 0.00% 41.49% NA
VI/Aromatic  96 64.60% 0.00% 0.00% 35.42% NA
Intermediate  90 26.70% 11.10% 3.33% 58.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402093212 T -> C LOC_Os04g04410.1 downstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:6.056; most accessible tissue: Callus, score: 21.946 N N N N
vg0402093212 T -> C LOC_Os04g04400.1 intron_variant ; MODIFIER silent_mutation Average:6.056; most accessible tissue: Callus, score: 21.946 N N N N
vg0402093212 T -> DEL N N silent_mutation Average:6.056; most accessible tissue: Callus, score: 21.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402093212 NA 1.11E-06 mr1164 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
vg0402093212 NA 2.87E-07 mr1077_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
vg0402093212 9.66E-06 9.65E-06 mr1147_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
vg0402093212 NA 1.20E-08 mr1149_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
vg0402093212 NA 9.30E-07 mr1206_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
vg0402093212 NA 5.16E-09 mr1229_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
vg0402093212 NA 1.44E-08 mr1441_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
vg0402093212 NA 1.87E-09 mr1521_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
vg0402093212 NA 3.66E-06 mr1596_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
vg0402093212 NA 7.57E-06 mr1617_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
vg0402093212 NA 2.56E-06 mr1763_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
vg0402093212 NA 9.63E-06 mr1840_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
vg0402093212 NA 1.62E-09 mr1880_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