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Detailed information for vg0133420260:

Variant ID: vg0133420260 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33420260
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, G: 0.42, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAGCTGGCAGTCCAATACGACAAGTGGAGCCTCAACATGGTCGAGCACACTCCCAGCCCACCCGCCACAGCCGAGCCACCCAAGAAAGTGATCAAAAC[A/G]
ACTAAGACGCCGAAACCAGACGGCGCAATCAAAATCGTCCCACTCTCCAGTGCCAACCCCGACAAGACGGTCAAGATCGGGGCATCACTGAACGAGAAAT

Reverse complement sequence

ATTTCTCGTTCAGTGATGCCCCGATCTTGACCGTCTTGTCGGGGTTGGCACTGGAGAGTGGGACGATTTTGATTGCGCCGTCTGGTTTCGGCGTCTTAGT[T/C]
GTTTTGATCACTTTCTTGGGTGGCTCGGCTGTGGCGGGTGGGCTGGGAGTGTGCTCGACCATGTTGAGGCTCCACTTGTCGTATTGGACTGCCAGCTTTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.50% 37.80% 3.62% 0.04% NA
All Indica  2759 94.30% 4.70% 0.91% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.00% 0.00% NA
Aus  269 42.80% 2.60% 53.90% 0.74% NA
Indica I  595 92.90% 6.40% 0.67% 0.00% NA
Indica II  465 97.60% 2.20% 0.22% 0.00% NA
Indica III  913 97.30% 2.50% 0.22% 0.00% NA
Indica Intermediate  786 90.10% 7.60% 2.29% 0.00% NA
Temperate Japonica  767 0.90% 99.10% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 28.90% 70.00% 1.11% 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
vg0133420260 A -> G LOC_Os01g57780.1 synonymous_variant ; p.Thr785Thr; LOW synonymous_codon Average:42.814; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 N N N N
vg0133420260 A -> G LOC_Os01g57780.1 synonymous_variant ; p.Thr785Thr; LOW nonsynonymous_codon ; T785M Average:42.814; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 probably damaging 2.771 TOLERATED 0.41
vg0133420260 A -> DEL LOC_Os01g57780.1 N frameshift_variant Average:42.814; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133420260 2.46E-10 5.43E-107 mr1008 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
vg0133420260 1.09E-08 1.61E-13 mr1008 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
vg0133420260 2.16E-10 1.16E-105 mr1009 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
vg0133420260 7.71E-09 3.55E-13 mr1009 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
vg0133420260 1.04E-07 6.86E-72 mr1014 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
vg0133420260 5.78E-06 1.92E-07 mr1014 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
vg0133420260 1.94E-07 NA mr1015 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
vg0133420260 5.90E-06 2.78E-07 mr1015 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
vg0133420260 NA 7.47E-11 mr1553 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
vg0133420260 NA 9.02E-09 mr1660 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
vg0133420260 NA 8.37E-07 mr1781 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
vg0133420260 NA 5.34E-08 mr1004_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
vg0133420260 NA 6.90E-08 mr1008_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