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Detailed information for vg0617909927:

Variant ID: vg0617909927 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17909927
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGACCAAGCACTGTGCGCCGATGGAGGCCGAGGAGTCGTGTGCCACTGCTGGCAGAGACTGAGGGACCAAGCGTTGCGCGTTGACGAAGGCCAAGGAGT[T/C]
GCATGCCGCCGCCAGTGAAGACGGAGGCTGAGGAGGAGTTGCGGCCGCCACGCGTGCGTTTGGTGGAGGCCGAGGATCAGGAGCCACGCGTCGTGTGCCG

Reverse complement sequence

CGGCACACGACGCGTGGCTCCTGATCCTCGGCCTCCACCAAACGCACGCGTGGCGGCCGCAACTCCTCCTCAGCCTCCGTCTTCACTGGCGGCGGCATGC[A/G]
ACTCCTTGGCCTTCGTCAACGCGCAACGCTTGGTCCCTCAGTCTCTGCCAGCAGTGGCACACGACTCCTCGGCCTCCATCGGCGCACAGTGCTTGGTCCC

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 97.10% 2.10% 0.83% 0.00% NA
All Indica  2759 99.40% 0.60% 0.04% 0.00% NA
All Japonica  1512 92.50% 5.20% 2.31% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 97.00% 0.10% 2.87% 0.00% NA
Tropical Japonica  504 84.90% 13.90% 1.19% 0.00% NA
Japonica Intermediate  241 94.20% 2.90% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 3.30% 3.33% 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
vg0617909927 T -> C LOC_Os06g30850.1 synonymous_variant ; p.Ala153Ala; LOW synonymous_codon Average:74.744; most accessible tissue: Zhenshan97 young leaf, score: 89.875 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617909927 2.17E-06 1.54E-07 mr1068_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
vg0617909927 NA 3.46E-06 mr1078_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
vg0617909927 NA 1.79E-06 mr1091_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
vg0617909927 5.56E-06 2.87E-08 mr1096_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
vg0617909927 NA 1.24E-06 mr1110_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
vg0617909927 NA 4.72E-06 mr1112_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
vg0617909927 NA 2.06E-07 mr1121_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
vg0617909927 NA 9.04E-07 mr1218_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
vg0617909927 7.34E-06 7.33E-06 mr1234_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
vg0617909927 NA 3.73E-06 mr1850_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