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Detailed information for vg0501533978:

Variant ID: vg0501533978 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1533978
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAAGGGTGTGTTTGTCACCCCTTCTTCCCAACCCCTCTCCCACATTTTCCGCACGCACACTTTTCAAACTGCTAAACGGTGTATTTTTTTTAAAAAAA[T/A]
TTCTATATGAAAGTTGCTTAAAAAACCAAATTAATCCATTTTTGAAAAAAATAGCTAACACTACTTAGTTAATCACACGCTAATGGACTGCTTCGTTTTC

Reverse complement sequence

GAAAACGAAGCAGTCCATTAGCGTGTGATTAACTAAGTAGTGTTAGCTATTTTTTTCAAAAATGGATTAATTTGGTTTTTTAAGCAACTTTCATATAGAA[A/T]
TTTTTTTAAAAAAAATACACCGTTTAGCAGTTTGAAAAGTGTGCGTGCGGAAAATGTGGGAGAGGGGTTGGGAAGAAGGGGTGACAAACACACCCTTAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 4.40% 1.29% 0.00% NA
All Indica  2759 90.40% 7.40% 2.14% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.10% 1.50% 1.34% 0.00% NA
Indica II  465 74.60% 19.80% 5.59% 0.00% NA
Indica III  913 97.80% 1.80% 0.44% 0.00% NA
Indica Intermediate  786 86.10% 11.20% 2.67% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 2.20% 2.22% 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
vg0501533978 T -> A LOC_Os05g03610.1 upstream_gene_variant ; 1730.0bp to feature; MODIFIER silent_mutation Average:44.872; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0501533978 T -> A LOC_Os05g03600.1 downstream_gene_variant ; 4271.0bp to feature; MODIFIER silent_mutation Average:44.872; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N
vg0501533978 T -> A LOC_Os05g03600-LOC_Os05g03610 intergenic_region ; MODIFIER silent_mutation Average:44.872; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501533978 NA 6.81E-06 mr1216 Ind_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
vg0501533978 5.00E-06 4.99E-06 mr1340 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
vg0501533978 2.15E-06 2.14E-06 mr1429 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
vg0501533978 5.13E-06 5.13E-06 mr1487 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