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Detailed information for vg0113081699:

Variant ID: vg0113081699 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13081699
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.65, T: 0.35, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:


CATTGATGAGGTCAAGAGCAGCTTCTTCGCTCATCCCATCTGCAAAGCCATCAATGGCATCAATGTCAACTCTTGGATAAAGGGATTTGGTCATCGCCAA[T/C]
GCCAGACTTGCTCCCATACTTCCAACTTCTTTGATGTTCTTGAAGTAAGTATCCGGAGCGACTCTCAGCTTGTCGAAGATTTCGGCAACATCAAGTGTAC

Reverse complement sequence

GTACACTTGATGTTGCCGAAATCTTCGACAAGCTGAGAGTCGCTCCGGATACTTACTTCAAGAACATCAAAGAAGTTGGAAGTATGGGAGCAAGTCTGGC[A/G]
TTGGCGATGACCAAATCCCTTTATCCAAGAGTTGACATTGATGCCATTGATGGCTTTGCAGATGGGATGAGCGAAGAAGCTGCTCTTGACCTCATCAATG

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 40.20% 3.60% 36.67% 19.55% NA
All Indica  2759 13.70% 0.10% 54.37% 31.82% NA
All Japonica  1512 87.80% 10.80% 1.06% 0.33% NA
Aus  269 45.40% 0.00% 51.67% 2.97% NA
Indica I  595 7.10% 0.00% 53.28% 39.66% NA
Indica II  465 9.20% 0.20% 49.68% 40.86% NA
Indica III  913 17.70% 0.20% 58.05% 23.99% NA
Indica Intermediate  786 16.70% 0.00% 53.69% 29.64% NA
Temperate Japonica  767 97.90% 1.20% 0.65% 0.26% NA
Tropical Japonica  504 68.80% 29.60% 1.39% 0.20% NA
Japonica Intermediate  241 95.40% 2.10% 1.66% 0.83% NA
VI/Aromatic  96 26.00% 0.00% 55.21% 18.75% NA
Intermediate  90 52.20% 3.30% 27.78% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113081699 T -> DEL LOC_Os01g23290.1 N frameshift_variant Average:12.465; most accessible tissue: Zhenshan97 young leaf, score: 18.918 N N N N
vg0113081699 T -> C LOC_Os01g23290.1 synonymous_variant ; p.Ala523Ala; LOW synonymous_codon Average:12.465; most accessible tissue: Zhenshan97 young leaf, score: 18.918 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113081699 NA 4.51E-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
vg0113081699 NA 4.02E-09 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
vg0113081699 NA 3.95E-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
vg0113081699 NA 4.23E-06 mr1949 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
vg0113081699 5.81E-06 5.81E-06 mr1076_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
vg0113081699 1.12E-06 NA mr1082_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
vg0113081699 NA 4.93E-08 mr1082_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
vg0113081699 3.81E-06 NA mr1083_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
vg0113081699 NA 2.95E-07 mr1083_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
vg0113081699 1.40E-07 NA mr1103_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
vg0113081699 2.61E-08 NA mr1104_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
vg0113081699 5.48E-07 NA mr1107_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
vg0113081699 6.06E-06 NA mr1226_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
vg0113081699 NA 2.49E-06 mr1226_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
vg0113081699 NA 1.35E-07 mr1227_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
vg0113081699 1.38E-06 NA mr1264_2 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