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Detailed information for vg0620536797:

Variant ID: vg0620536797 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20536797
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGATTGCTGTTGACCAAAAATTTGCATGCCATGAGTTTCCTGAGAACACTAGAGTTAGAGCTGCTACTAGTGAGTTCATCGATTTTGCTTTGGTTTGGT[G/A]
GATAGAACATGGCAAGAAAAATCCTAATAACATGCCACAAACTTGGGATGCTTTGAAACGGGTCATGCGGGCTAGATTTGTTCCTTCTTACTATACACGT

Reverse complement sequence

ACGTGTATAGTAAGAAGGAACAAATCTAGCCCGCATGACCCGTTTCAAAGCATCCCAAGTTTGTGGCATGTTATTAGGATTTTTCTTGCCATGTTCTATC[C/T]
ACCAAACCAAAGCAAAATCGATGAACTCACTAGTAGCAGCTCTAACTCTAGTGTTCTCAGGAAACTCATGGCATGCAAATTTTTGGTCAACAGCAATCTC

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 25.60% 1.30% 9.01% 64.05% NA
All Indica  2759 10.00% 0.10% 8.95% 81.01% NA
All Japonica  1512 42.00% 3.80% 6.15% 48.02% NA
Aus  269 88.50% 0.00% 6.32% 5.20% NA
Indica I  595 8.40% 0.00% 7.23% 84.37% NA
Indica II  465 9.20% 0.00% 7.53% 83.23% NA
Indica III  913 7.70% 0.10% 10.51% 81.71% NA
Indica Intermediate  786 14.20% 0.10% 9.29% 76.34% NA
Temperate Japonica  767 72.90% 0.80% 5.35% 20.99% NA
Tropical Japonica  504 6.30% 1.60% 3.37% 88.69% NA
Japonica Intermediate  241 18.30% 18.30% 14.52% 48.96% NA
VI/Aromatic  96 39.60% 0.00% 53.12% 7.29% NA
Intermediate  90 27.80% 2.20% 20.00% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620536797 G -> A LOC_Os06g35210.1 N stop_gained Average:13.233; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N
vg0620536797 G -> DEL LOC_Os06g35210.1 N frameshift_variant Average:13.233; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620536797 NA 4.97E-07 mr1403 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
vg0620536797 1.91E-06 1.91E-06 mr1520 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
vg0620536797 NA 8.95E-06 mr1729 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
vg0620536797 NA 3.56E-06 mr1082_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
vg0620536797 NA 4.80E-06 mr1083_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
vg0620536797 4.92E-08 1.11E-12 mr1408_2 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
vg0620536797 NA 6.37E-08 mr1408_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