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Detailed information for vg0608661476:

Variant ID: vg0608661476 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8661476
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATAGTCGTGGATGACGAGCGGTGACTCGTAGAGGCGGCGATGGAGGATCGGCAGGCAGAGTGGTCATGGTCGATGGGGATCGGCGGTGGCGTGGCTAC[G/A]
GAAGACGGGCAGTGACTCTTGGAGGCGCCGTGGGCAACGGTCGACGGGGAGAACCGGCGACATCCAACTTTGAACCGGCGACGGAGATCGGCGGCTGTGT

Reverse complement sequence

ACACAGCCGCCGATCTCCGTCGCCGGTTCAAAGTTGGATGTCGCCGGTTCTCCCCGTCGACCGTTGCCCACGGCGCCTCCAAGAGTCACTGCCCGTCTTC[C/T]
GTAGCCACGCCACCGCCGATCCCCATCGACCATGACCACTCTGCCTGCCGATCCTCCATCGCCGCCTCTACGAGTCACCGCTCGTCATCCACGACTATGT

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 61.30% 3.30% 1.23% 34.19% NA
All Indica  2759 41.10% 0.30% 1.49% 57.09% NA
All Japonica  1512 88.40% 9.80% 0.93% 0.86% NA
Aus  269 99.30% 0.00% 0.37% 0.37% NA
Indica I  595 43.90% 0.20% 0.67% 55.29% NA
Indica II  465 21.30% 1.50% 1.51% 75.70% NA
Indica III  913 55.40% 0.00% 1.10% 43.48% NA
Indica Intermediate  786 34.20% 0.00% 2.54% 63.23% NA
Temperate Japonica  767 84.60% 13.40% 1.04% 0.91% NA
Tropical Japonica  504 93.50% 5.00% 0.99% 0.60% NA
Japonica Intermediate  241 90.00% 8.30% 0.41% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 66.70% 1.10% 2.22% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608661476 G -> A LOC_Os06g15260.1 intron_variant ; MODIFIER silent_mutation Average:46.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 N N N N
vg0608661476 G -> DEL N N silent_mutation Average:46.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608661476 NA 1.66E-06 mr1028 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
vg0608661476 NA 7.72E-07 mr1186 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
vg0608661476 6.82E-07 6.82E-07 mr1373 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
vg0608661476 NA 1.28E-06 mr1616 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
vg0608661476 NA 1.24E-06 mr1648 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
vg0608661476 NA 3.22E-06 mr1652 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
vg0608661476 NA 1.44E-06 mr1921 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