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Detailed information for vg0318534639:

Variant ID: vg0318534639 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18534639
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: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTCGGCTTGGGGATAAGATGATGTCCGTGATGGTCAGATATCATGCGGGATACTTAGGCTAAAGTTCAATGCACGTGGTTGGTGAAGATTCCATATGG[T/C]
ATACGATGGAGGTATTGTGTGCGTGTGGGATGCGGAGTCGAATTTGGAAGGAGTCCAAATTTGGTATGATTGGAGTTTGTAAAATTTGTTTCTTGTACAA

Reverse complement sequence

TTGTACAAGAAACAAATTTTACAAACTCCAATCATACCAAATTTGGACTCCTTCCAAATTCGACTCCGCATCCCACACGCACACAATACCTCCATCGTAT[A/G]
CCATATGGAATCTTCACCAACCACGTGCATTGAACTTTAGCCTAAGTATCCCGCATGATATCTGACCATCACGGACATCATCTTATCCCCAAGCCGACTC

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 69.10% 30.60% 0.13% 0.17% NA
All Indica  2759 97.80% 2.00% 0.07% 0.14% NA
All Japonica  1512 16.10% 83.60% 0.13% 0.13% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 98.70% 0.80% 0.17% 0.34% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.60% 0.13% 0.25% NA
Temperate Japonica  767 0.30% 99.60% 0.00% 0.13% NA
Tropical Japonica  504 39.90% 59.70% 0.20% 0.20% NA
Japonica Intermediate  241 17.00% 82.60% 0.41% 0.00% NA
VI/Aromatic  96 28.10% 71.90% 0.00% 0.00% NA
Intermediate  90 55.60% 40.00% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318534639 T -> C LOC_Os03g32410.1 upstream_gene_variant ; 719.0bp to feature; MODIFIER silent_mutation Average:44.603; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0318534639 T -> C LOC_Os03g32420.1 upstream_gene_variant ; 4176.0bp to feature; MODIFIER silent_mutation Average:44.603; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0318534639 T -> C LOC_Os03g32400.1 downstream_gene_variant ; 3178.0bp to feature; MODIFIER silent_mutation Average:44.603; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0318534639 T -> C LOC_Os03g32400-LOC_Os03g32410 intergenic_region ; MODIFIER silent_mutation Average:44.603; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0318534639 T -> DEL N N silent_mutation Average:44.603; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318534639 NA 1.71E-07 mr1217 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
vg0318534639 NA 1.25E-07 mr1227 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
vg0318534639 NA 3.64E-21 mr1588 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
vg0318534639 NA 3.79E-06 mr1588 Ind_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
vg0318534639 NA 1.08E-08 mr1718 Ind_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
vg0318534639 NA 1.55E-11 mr1750 Ind_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
vg0318534639 NA 4.81E-07 mr1845 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
vg0318534639 NA 4.16E-08 mr1852 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
vg0318534639 NA 9.14E-13 mr1853 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
vg0318534639 NA 2.04E-06 mr1188_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
vg0318534639 NA 5.80E-28 mr1588_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
vg0318534639 2.27E-08 8.56E-11 mr1588_2 Ind_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
vg0318534639 2.41E-07 1.13E-14 mr1718_2 Ind_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
vg0318534639 NA 4.02E-18 mr1750_2 Ind_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
vg0318534639 NA 1.35E-13 mr1827_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