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Detailed information for vg0811905123:

Variant ID: vg0811905123 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 11905123
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACTGAACCTTAATACTTCATATATAGGACCTGTGATAGCAAGAATATTCTCAACATTATTCCAAAAGTCCTCACAATTGATTTCTTGAACAATGGCTCT[T/A]
GCTTGCTGCCGCAGATCATTGGTGCAACCTTTCATCCAATCTTTCCATTGATTGGTGACTATGGTGGTGGCAAGTGCTTCTTGACATTTAGTGAGCCTCA

Reverse complement sequence

TGAGGCTCACTAAATGTCAAGAAGCACTTGCCACCACCATAGTCACCAATCAATGGAAAGATTGGATGAAAGGTTGCACCAATGATCTGCGGCAGCAAGC[A/T]
AGAGCCATTGTTCAAGAAATCAATTGTGAGGACTTTTGGAATAATGTTGAGAATATTCTTGCTATCACAGGTCCTATATATGAAGTATTAAGGTTCAGTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.70% 39.80% 1.74% 8.84% NA
All Indica  2759 81.20% 6.70% 2.75% 9.39% NA
All Japonica  1512 2.20% 88.10% 0.00% 9.72% NA
Aus  269 15.60% 83.30% 0.74% 0.37% NA
Indica I  595 94.50% 0.30% 2.86% 2.35% NA
Indica II  465 85.80% 7.50% 1.51% 5.16% NA
Indica III  913 72.90% 6.40% 3.83% 16.87% NA
Indica Intermediate  786 78.00% 11.30% 2.16% 8.52% NA
Temperate Japonica  767 2.00% 97.80% 0.00% 0.26% NA
Tropical Japonica  504 1.60% 72.60% 0.00% 25.79% NA
Japonica Intermediate  241 4.10% 89.60% 0.00% 6.22% NA
VI/Aromatic  96 2.10% 90.60% 0.00% 7.29% NA
Intermediate  90 33.30% 57.80% 4.44% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0811905123 T -> A LOC_Os08g19870.1 synonymous_variant ; p.Ala411Ala; LOW synonymous_codon Average:50.869; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 N N N N
vg0811905123 T -> A LOC_Os08g19870.1 synonymous_variant ; p.Ala411Ala; LOW nonsynonymous_codon ; A411V Average:50.869; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 unknown unknown DELETERIOUS 0.02
vg0811905123 T -> DEL LOC_Os08g19870.1 N frameshift_variant Average:50.869; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0811905123 NA 4.21E-09 mr1134 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
vg0811905123 8.68E-06 NA 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
vg0811905123 NA 1.14E-08 mr1135 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
vg0811905123 NA 1.09E-22 mr1422 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
vg0811905123 NA 9.64E-10 mr1504 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
vg0811905123 NA 1.67E-18 mr1583 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
vg0811905123 NA 6.76E-06 mr1672 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
vg0811905123 NA 6.65E-15 mr1870 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
vg0811905123 NA 5.47E-07 mr1134_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
vg0811905123 NA 5.01E-10 mr1134_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
vg0811905123 NA 1.45E-07 mr1215_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
vg0811905123 NA 2.21E-19 mr1218_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
vg0811905123 NA 6.71E-27 mr1422_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
vg0811905123 NA 1.65E-14 mr1583_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
vg0811905123 NA 7.65E-07 mr1672_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
vg0811905123 NA 6.86E-14 mr1850_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