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Detailed information for vg1116613245:

Variant ID: vg1116613245 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16613245
Reference Allele: TAlternative Allele: C,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


CAATCCAACTGGACAGACAGGTTCTCGCAAGAGAAAACTGGTGCTCGACAACGATGAAGGCGACGACGATAAATCTGGGGACAAGGGCTCGCCTAATAAA[T/C,A]
TCCCAAAGCGTACCATGCCCAAGAAAAAACTGGCTGGCCGTCAAATGCTAAAGATTAGAACATCTTCCAGGTATAAACCTCTCGGTACCATCTCCCTTTG

Reverse complement sequence

CAAAGGGAGATGGTACCGAGAGGTTTATACCTGGAAGATGTTCTAATCTTTAGCATTTGACGGCCAGCCAGTTTTTTCTTGGGCATGGTACGCTTTGGGA[A/G,T]
TTTATTAGGCGAGCCCTTGTCCCCAGATTTATCGTCGTCGCCTTCATCGTTGTCGAGCACCAGTTTTCTCTTGCGAGAACCTGTCTGTCCAGTTGGATTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 24.00% 7.60% 53.09% 14.03% A: 1.25%
All Indica  2759 7.00% 5.00% 62.56% 23.45% A: 1.92%
All Japonica  1512 52.00% 11.90% 35.38% 0.33% A: 0.40%
Aus  269 15.20% 13.00% 70.26% 1.49% NA
Indica I  595 7.60% 2.20% 45.88% 44.20% A: 0.17%
Indica II  465 4.50% 2.40% 58.49% 31.61% A: 3.01%
Indica III  913 5.50% 8.70% 74.26% 8.87% A: 2.74%
Indica Intermediate  786 9.90% 4.60% 63.99% 19.85% A: 1.65%
Temperate Japonica  767 86.70% 0.80% 11.99% 0.52% NA
Tropical Japonica  504 10.70% 22.80% 65.48% 0.00% A: 0.99%
Japonica Intermediate  241 27.80% 24.50% 46.89% 0.41% A: 0.41%
VI/Aromatic  96 93.80% 0.00% 6.25% 0.00% NA
Intermediate  90 25.60% 7.80% 58.89% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1116613245 T -> A LOC_Os11g28720.1 missense_variant ; p.Phe368Ile; MODERATE nonsynonymous_codon ; F368T Average:13.238; most accessible tissue: Minghui63 panicle, score: 25.313 benign 1.177 TOLERATED 0.23
vg1116613245 T -> DEL LOC_Os11g28720.1 N frameshift_variant Average:13.238; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1116613245 T -> C LOC_Os11g28720.1 missense_variant ; p.Phe368Leu; MODERATE nonsynonymous_codon ; F368P Average:13.238; most accessible tissue: Minghui63 panicle, score: 25.313 benign -0.141 TOLERATED 0.29
vg1116613245 T -> C LOC_Os11g28720.1 missense_variant ; p.Phe368Leu; MODERATE nonsynonymous_codon ; F368L Average:13.238; most accessible tissue: Minghui63 panicle, score: 25.313 benign -0.226 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116613245 NA 7.79E-07 mr1076 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
vg1116613245 NA 1.51E-07 mr1082 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
vg1116613245 NA 5.57E-08 mr1083 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
vg1116613245 NA 1.85E-06 mr1226 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
vg1116613245 NA 2.06E-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
vg1116613245 NA 2.03E-06 mr1227 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
vg1116613245 9.18E-06 NA mr1299 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
vg1116613245 7.28E-07 7.28E-07 mr1299 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
vg1116613245 NA 7.76E-06 mr1408 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
vg1116613245 NA 2.55E-07 mr1560 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
vg1116613245 NA 1.23E-07 mr1639 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
vg1116613245 NA 5.53E-07 mr1860 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
vg1116613245 2.95E-06 2.95E-06 mr1881 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
vg1116613245 3.64E-06 3.64E-06 mr1159_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
vg1116613245 NA 8.03E-06 mr1267_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
vg1116613245 2.43E-06 2.43E-06 mr1312_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
vg1116613245 3.48E-06 3.48E-06 mr1663_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
vg1116613245 5.38E-06 5.38E-06 mr1688_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
vg1116613245 NA 5.49E-07 mr1812_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
vg1116613245 1.55E-06 1.55E-06 mr1832_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
vg1116613245 NA 1.89E-06 mr1833_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
vg1116613245 9.38E-07 9.38E-07 mr1843_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
vg1116613245 3.59E-06 3.59E-06 mr1847_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