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Detailed information for vg0602466917:

Variant ID: vg0602466917 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2466917
Reference Allele: GAlternative Allele: A,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTCCTTGGAAAGCTCTACAATGTCTAACATGGCATTCACCATCTCAGTTAGAGTACGATTCTTTCTTTCGGCCACCCCATTTGATTGGGGTGAATAGG[G/A,C]
AGGCGTCCTCTCATGAATAATTCCAAACTCTTCGCAAAAGGATGAAAATTCATTGGAAAAATACTCCCCACCTCTATCAGACCTCAACCGTTTGATTTTC

Reverse complement sequence

GAAAATCAAACGGTTGAGGTCTGATAGAGGTGGGGAGTATTTTTCCAATGAATTTTCATCCTTTTGCGAAGAGTTTGGAATTATTCATGAGAGGACGCCT[C/T,G]
CCTATTCACCCCAATCAAATGGGGTGGCCGAAAGAAAGAATCGTACTCTAACTGAGATGGTGAATGCCATGTTAGACATTGTAGAGCTTTCCAAGGAATG

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 93.30% 3.40% 0.95% 2.31% C: 0.04%
All Indica  2759 98.00% 0.00% 0.22% 1.74% C: 0.07%
All Japonica  1512 88.50% 10.20% 1.26% 0.07% NA
Aus  269 71.40% 0.00% 7.43% 21.19% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 96.90% 0.00% 0.33% 2.52% C: 0.22%
Indica Intermediate  786 96.70% 0.00% 0.38% 2.93% NA
Temperate Japonica  767 98.20% 0.30% 1.43% 0.13% NA
Tropical Japonica  504 75.20% 24.20% 0.60% 0.00% NA
Japonica Intermediate  241 85.50% 12.40% 2.07% 0.00% NA
VI/Aromatic  96 95.80% 2.10% 0.00% 2.08% NA
Intermediate  90 95.60% 3.30% 0.00% 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
vg0602466917 G -> C LOC_Os06g05460.1 missense_variant ; p.Pro571Ala; MODERATE nonsynonymous_codon ; P571A Average:22.61; most accessible tissue: Minghui63 flag leaf, score: 42.036 benign 1.311 DELETERIOUS 0.00
vg0602466917 G -> A LOC_Os06g05460.1 missense_variant ; p.Pro571Ser; MODERATE nonsynonymous_codon ; P571S Average:22.61; most accessible tissue: Minghui63 flag leaf, score: 42.036 benign 1.494 DELETERIOUS 0.01
vg0602466917 G -> DEL LOC_Os06g05460.1 N frameshift_variant Average:22.61; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602466917 3.42E-06 4.07E-07 mr1745 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
vg0602466917 NA 7.44E-06 mr1745_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