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Detailed information for vg1116465115:

Variant ID: vg1116465115 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16465115
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTACAACACATGGTTTCTTAAAGTGGTCCATTAATAAATACATCATCTCTCTTCTGTACCAATCATATTTATTCTTCATATATTATGAAGACACTATT[A/C]
TTTACCAATGCAAAACTTGATAGTGTCTAGTGCATAGGTTCTCGTGTTGAAGCTGTCTCTTGCATGAGACCCAGTTTTTTCCTCTCTTCACTATCTCTCT

Reverse complement sequence

AGAGAGATAGTGAAGAGAGGAAAAAACTGGGTCTCATGCAAGAGACAGCTTCAACACGAGAACCTATGCACTAGACACTATCAAGTTTTGCATTGGTAAA[T/G]
AATAGTGTCTTCATAATATATGAAGAATAAATATGATTGGTACAGAAGAGAGATGATGTATTTATTAATGGACCACTTTAAGAAACCATGTGTTGTAGAG

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 65.50% 34.20% 0.34% 0.00% NA
All Indica  2759 98.40% 1.20% 0.33% 0.00% NA
All Japonica  1512 4.40% 95.40% 0.26% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 98.80% 0.80% 0.34% 0.00% NA
Indica II  465 99.10% 0.40% 0.43% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 96.80% 2.70% 0.51% 0.00% NA
Temperate Japonica  767 2.90% 96.90% 0.26% 0.00% NA
Tropical Japonica  504 6.90% 92.70% 0.40% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 88.50% 1.04% 0.00% NA
Intermediate  90 57.80% 40.00% 2.22% 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
vg1116465115 A -> C LOC_Os11g28550.1 downstream_gene_variant ; 3321.0bp to feature; MODIFIER silent_mutation Average:43.447; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1116465115 A -> C LOC_Os11g28540-LOC_Os11g28550 intergenic_region ; MODIFIER silent_mutation Average:43.447; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116465115 NA 5.35E-19 Yield All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1116465115 NA 1.73E-78 mr1135 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
vg1116465115 NA 6.24E-24 mr1375 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
vg1116465115 NA 3.18E-23 mr1383 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
vg1116465115 NA 2.50E-87 mr1504 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
vg1116465115 NA 7.68E-89 mr1517 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
vg1116465115 NA 1.48E-88 mr1672 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
vg1116465115 NA 1.39E-21 mr1698 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
vg1116465115 3.62E-07 5.07E-103 mr1758 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
vg1116465115 1.18E-06 1.18E-06 mr1758 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
vg1116465115 NA 6.81E-07 mr1797 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
vg1116465115 NA 6.81E-07 mr1801 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
vg1116465115 NA 1.30E-40 mr1873 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
vg1116465115 NA 2.29E-38 mr1541_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
vg1116465115 5.59E-11 2.19E-147 mr1758_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
vg1116465115 9.41E-09 5.28E-12 mr1758_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