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Detailed information for vg0817397543:

Variant ID: vg0817397543 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17397543
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAACAAATAACATTAAAGAACTTCGTCGTGATATTTTCAAAAAGGAGTATATTAAATTTGAGATGAAACCTGGAGAAGCTTTGGATGACTATCTCTCTA[A/G]
GTTTAATAAAATTTTGAGTGATCTTAGATCTATTGATTCTTCTTATGGTGCTAATTATCCACAATATGAGATTTCTCGTCACTTTTTGAACGGTCTTGAT

Reverse complement sequence

ATCAAGACCGTTCAAAAAGTGACGAGAAATCTCATATTGTGGATAATTAGCACCATAAGAAGAATCAATAGATCTAAGATCACTCAAAATTTTATTAAAC[T/C]
TAGAGAGATAGTCATCCAAAGCTTCTCCAGGTTTCATCTCAAATTTAATATACTCCTTTTTGAAAATATCACGACGAAGTTCTTTAATGTTATTTGTTCC

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 61.20% 27.40% 8.93% 2.43% NA
All Indica  2759 88.30% 2.70% 8.05% 0.91% NA
All Japonica  1512 10.40% 73.10% 10.98% 5.56% NA
Aus  269 94.40% 0.40% 5.20% 0.00% NA
Indica I  595 87.20% 4.00% 8.57% 0.17% NA
Indica II  465 81.70% 3.70% 12.26% 2.37% NA
Indica III  913 93.30% 1.10% 5.15% 0.44% NA
Indica Intermediate  786 87.30% 3.10% 8.52% 1.15% NA
Temperate Japonica  767 5.50% 75.00% 13.95% 5.61% NA
Tropical Japonica  504 16.10% 67.90% 8.93% 7.14% NA
Japonica Intermediate  241 14.10% 78.00% 5.81% 2.07% NA
VI/Aromatic  96 8.30% 77.10% 9.38% 5.21% NA
Intermediate  90 41.10% 45.60% 12.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817397543 A -> G LOC_Os08g28500.1 missense_variant ; p.Lys134Arg; MODERATE nonsynonymous_codon ; K134R Average:13.589; most accessible tissue: Callus, score: 26.053 unknown unknown TOLERATED 1.00
vg0817397543 A -> DEL LOC_Os08g28500.1 N frameshift_variant Average:13.589; most accessible tissue: Callus, score: 26.053 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817397543 NA 2.42E-09 mr1198 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
vg0817397543 NA 2.78E-10 mr1623 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
vg0817397543 NA 6.85E-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
vg0817397543 NA 2.49E-06 mr1080_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
vg0817397543 NA 4.93E-10 mr1299_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
vg0817397543 NA 4.67E-11 mr1537_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
vg0817397543 NA 5.45E-17 mr1592_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
vg0817397543 NA 4.47E-12 mr1595_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
vg0817397543 NA 2.25E-08 mr1600_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
vg0817397543 2.02E-06 5.59E-07 mr1619_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
vg0817397543 NA 1.37E-08 mr1700_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
vg0817397543 NA 1.33E-12 mr1713_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
vg0817397543 NA 8.22E-08 mr1727_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
vg0817397543 NA 1.15E-07 mr1783_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
vg0817397543 NA 4.58E-07 mr1840_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
vg0817397543 NA 1.28E-06 mr1856_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
vg0817397543 NA 2.35E-09 mr1905_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
vg0817397543 NA 6.70E-09 mr1947_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