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Detailed information for vg1100988116:

Variant ID: vg1100988116 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 988116
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, C: 0.13, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGATGAGATCGAAGGTGACAAGACAAAAAGGTTGCTTAAGGGCAAAGCTGGTACATCTGCCTCAATAAATATGGTTTTCATGTTACCTGCAGAATTCG[A/C]
GGCTAGGCAAGCCGATGTTGATGATGTTGAAGAAGCTTCGGCTAAATTGGTTTGTCTCGAGAGCAAGCAGTTTTTGAGAAGCCAGAAGGGACAGAGAATC

Reverse complement sequence

GATTCTCTGTCCCTTCTGGCTTCTCAAAAACTGCTTGCTCTCGAGACAAACCAATTTAGCCGAAGCTTCTTCAACATCATCAACATCGGCTTGCCTAGCC[T/G]
CGAATTCTGCAGGTAACATGAAAACCATATTTATTGAGGCAGATGTACCAGCTTTGCCCTTAAGCAACCTTTTTGTCTTGTCACCTTCGATCTCATCAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.30% 35.90% 1.33% 2.45% NA
All Indica  2759 93.00% 3.90% 1.70% 1.34% NA
All Japonica  1512 2.00% 97.70% 0.13% 0.20% NA
Aus  269 56.50% 13.80% 4.09% 25.65% NA
Indica I  595 97.30% 0.80% 1.51% 0.34% NA
Indica II  465 84.30% 12.70% 1.51% 1.51% NA
Indica III  913 96.90% 0.50% 1.53% 0.99% NA
Indica Intermediate  786 90.50% 5.00% 2.16% 2.42% NA
Temperate Japonica  767 2.50% 97.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.60% 0.20% 0.20% NA
Japonica Intermediate  241 2.50% 96.30% 0.41% 0.83% NA
VI/Aromatic  96 68.80% 25.00% 1.04% 5.21% NA
Intermediate  90 40.00% 55.60% 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
vg1100988116 A -> DEL N N silent_mutation Average:40.306; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg1100988116 A -> C LOC_Os11g02880.1 downstream_gene_variant ; 4169.0bp to feature; MODIFIER silent_mutation Average:40.306; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N
vg1100988116 A -> C LOC_Os11g02890.1 intron_variant ; MODIFIER silent_mutation Average:40.306; most accessible tissue: Zhenshan97 young leaf, score: 74.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100988116 NA 2.39E-10 mr1023 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
vg1100988116 NA 1.75E-09 mr1093 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
vg1100988116 NA 8.25E-06 mr1103 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
vg1100988116 NA 1.44E-11 mr1142 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
vg1100988116 NA 2.41E-07 mr1235 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
vg1100988116 NA 7.79E-07 mr1241 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
vg1100988116 NA 5.40E-32 mr1243 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
vg1100988116 NA 3.38E-06 mr1257 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
vg1100988116 1.80E-06 1.14E-06 mr1395 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
vg1100988116 NA 1.11E-25 mr1411 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
vg1100988116 NA 1.97E-06 mr1423 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
vg1100988116 NA 3.38E-06 mr1435 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
vg1100988116 NA 9.41E-06 mr1446 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
vg1100988116 NA 2.59E-09 mr1489 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
vg1100988116 NA 8.52E-22 mr1541 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
vg1100988116 NA 1.88E-06 mr1599 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
vg1100988116 9.41E-06 NA mr1629 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
vg1100988116 NA 2.95E-34 mr1733 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
vg1100988116 NA 9.25E-30 mr1737 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
vg1100988116 2.99E-07 NA mr1758 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
vg1100988116 3.59E-06 NA mr1758 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
vg1100988116 NA 1.76E-08 mr1805 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
vg1100988116 NA 1.26E-10 mr1819 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
vg1100988116 NA 9.00E-14 mr1982 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
vg1100988116 NA 1.76E-12 mr1377_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
vg1100988116 NA 5.67E-09 mr1379_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
vg1100988116 NA 8.77E-08 mr1819_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