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Detailed information for vg1018298010:

Variant ID: vg1018298010 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 18298010
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, A: 0.31, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TAACAGGTGAGGACATTGCTATTGCTGAGATTGCAATCTCTTCTGTCATTTGTATGGGCATTAACAATAGATGGGATAAGAAATTTACACAAGAGACCGT[T/A]
AACTATCTGCAGTTACTTTGGTACGTTAGTCTTACCTAGACTAGATGCTCAATTGGCCAGAATCAAGGGGCCAGGCCCATCTTCAAAAGCCATGGTGAAT

Reverse complement sequence

ATTCACCATGGCTTTTGAAGATGGGCCTGGCCCCTTGATTCTGGCCAATTGAGCATCTAGTCTAGGTAAGACTAACGTACCAAAGTAACTGCAGATAGTT[A/T]
ACGGTCTCTTGTGTAAATTTCTTATCCCATCTATTGTTAATGCCCATACAAATGACAGAAGAGATTGCAATCTCAGCAATAGCAATGTCCTCACCTGTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.10% 43.80% 0.13% 0.06% NA
All Indica  2759 70.10% 29.50% 0.22% 0.11% NA
All Japonica  1512 25.70% 74.30% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 87.10% 12.80% 0.17% 0.00% NA
Indica II  465 83.70% 16.10% 0.22% 0.00% NA
Indica III  913 51.60% 47.80% 0.44% 0.22% NA
Indica Intermediate  786 70.90% 29.00% 0.00% 0.13% NA
Temperate Japonica  767 4.20% 95.80% 0.00% 0.00% NA
Tropical Japonica  504 65.70% 34.30% 0.00% 0.00% NA
Japonica Intermediate  241 10.80% 89.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 57.80% 42.20% 0.00% 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
vg1018298010 T -> A LOC_Os10g34310.1 3_prime_UTR_variant ; 373.0bp to feature; MODIFIER silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N
vg1018298010 T -> A LOC_Os10g34310.2 3_prime_UTR_variant ; 373.0bp to feature; MODIFIER silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N
vg1018298010 T -> A LOC_Os10g34300.1 upstream_gene_variant ; 812.0bp to feature; MODIFIER silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N
vg1018298010 T -> A LOC_Os10g34290.1 downstream_gene_variant ; 3834.0bp to feature; MODIFIER silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N
vg1018298010 T -> A LOC_Os10g34320.1 downstream_gene_variant ; 3428.0bp to feature; MODIFIER silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N
vg1018298010 T -> DEL N N silent_mutation Average:50.446; most accessible tissue: Callus, score: 91.645 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1018298010 NA 1.11E-12 mr1016 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
vg1018298010 NA 5.44E-12 mr1017 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
vg1018298010 NA 8.94E-11 mr1018 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
vg1018298010 NA 1.66E-08 mr1019 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
vg1018298010 NA 6.52E-14 mr1055 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
vg1018298010 NA 1.99E-08 mr1129 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
vg1018298010 NA 9.17E-11 mr1132 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
vg1018298010 NA 1.06E-10 mr1178 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
vg1018298010 NA 5.23E-12 mr1390 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
vg1018298010 NA 7.68E-12 mr1490 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
vg1018298010 NA 7.44E-15 mr1771 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
vg1018298010 NA 6.79E-12 mr1019_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
vg1018298010 NA 4.15E-09 mr1022_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
vg1018298010 9.29E-06 2.38E-15 mr1055_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
vg1018298010 3.71E-06 1.12E-16 mr1132_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
vg1018298010 NA 7.26E-18 mr1178_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
vg1018298010 NA 2.74E-09 mr1261_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
vg1018298010 NA 8.92E-16 mr1390_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
vg1018298010 NA 1.18E-16 mr1490_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
vg1018298010 NA 6.35E-07 mr1632_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