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Detailed information for vg0500016244:

Variant ID: vg0500016244 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16244
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATCCGTGCCACGGGAGCGAAGGCATCGTCGTAGTCGATCCCCTCCTGCTGCACGAAACCGCGTGCCACCAAGCGAGCCTTGTGCTTGACGATGGCTCT[A/G]
GCTTCATCCCTCTTCAGCTTGAACACCCACTTAAGGGTGATCCCGCGGTGACCACGAGGGAGGTCAGCAAGCTCCCAGGTGCGGTTCTCCTGAACCGCGT

Reverse complement sequence

ACGCGGTTCAGGAGAACCGCACCTGGGAGCTTGCTGACCTCCCTCGTGGTCACCGCGGGATCACCCTTAAGTGGGTGTTCAAGCTGAAGAGGGATGAAGC[T/C]
AGAGCCATCGTCAAGCACAAGGCTCGCTTGGTGGCACGCGGTTTCGTGCAGCAGGAGGGGATCGACTACGACGATGCCTTCGCTCCCGTGGCACGGATGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.00% 0.80% 20.91% 41.37% NA
All Indica  2759 4.90% 1.20% 33.38% 60.53% NA
All Japonica  1512 96.40% 0.00% 0.20% 3.37% NA
Aus  269 4.50% 0.40% 19.70% 75.46% NA
Indica I  595 2.50% 0.80% 13.28% 83.36% NA
Indica II  465 6.00% 2.20% 20.43% 71.40% NA
Indica III  913 3.70% 0.10% 56.08% 40.09% NA
Indica Intermediate  786 7.50% 2.00% 29.90% 60.56% NA
Temperate Japonica  767 94.50% 0.00% 0.26% 5.22% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 95.40% 0.00% 0.00% 4.56% NA
VI/Aromatic  96 90.60% 0.00% 0.00% 9.38% NA
Intermediate  90 60.00% 3.30% 12.22% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0500016244 A -> DEL LOC_Os05g00996.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500016244 A -> G LOC_Os05g00996.1 synonymous_variant ; p.Ala551Ala; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500016244 NA 5.09E-06 mr1334 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
vg0500016244 NA 1.47E-06 mr1527 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
vg0500016244 NA 6.27E-06 mr1718 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
vg0500016244 NA 6.38E-06 mr1750 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
vg0500016244 NA 2.17E-24 mr1588_2 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
vg0500016244 4.94E-06 NA mr1718_2 Ind_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