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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0105166660:

Variant ID: vg0105166660 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5166660
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAGACAAGGCGTCGATACTGATCAGGGCAAGAGAGCACATAAAGTCTCTCGAGTCAAAGCTGTCGGAGCTGGAGGAGAAGAACCGGGAGCTGGAGGCG[A/C]
GGCTAGCCAGCCGCCCCGCCGCCAAGAACGACAAAGGCGAGACGGCGGCGGCGGAAGCCGGCGACGAGACGAAGCGAGAGGACCTAGTAGAGATCGAGGT

Reverse complement sequence

ACCTCGATCTCTACTAGGTCCTCTCGCTTCGTCTCGTCGCCGGCTTCCGCCGCCGCCGTCTCGCCTTTGTCGTTCTTGGCGGCGGGGCGGCTGGCTAGCC[T/G]
CGCCTCCAGCTCCCGGTTCTTCTCCTCCAGCTCCGACAGCTTTGACTCGAGAGACTTTATGTGCTCTCTTGCCCTGATCAGTATCGACGCCTTGTCTTTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.60% 7.30% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 78.30% 21.60% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 85.10% 14.60% 0.26% 0.00% NA
Tropical Japonica  504 66.10% 33.90% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0105166660 A -> C LOC_Os01g09930.1 synonymous_variant ; p.Arg246Arg; LOW synonymous_codon Average:58.877; most accessible tissue: Zhenshan97 root, score: 83.426 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105166660 1.78E-24 1.48E-26 mr1057 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
vg0105166660 1.19E-14 1.36E-20 mr1057 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
vg0105166660 2.76E-06 NA mr1238 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
vg0105166660 9.87E-06 NA mr1309 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
vg0105166660 1.67E-06 NA mr1677 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
vg0105166660 NA 2.93E-06 mr1677 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
vg0105166660 2.05E-33 1.13E-38 mr1057_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
vg0105166660 2.81E-18 1.41E-23 mr1057_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
vg0105166660 6.70E-07 NA mr1238_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
vg0105166660 6.53E-06 NA mr1484_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
vg0105166660 6.96E-07 NA mr1841_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