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Detailed information for vg0115667573:

Variant ID: vg0115667573 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 15667573
Reference Allele: TAlternative Allele: C,A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACCTGAGGTACAACATCAGGGAAGAGATCTGTCATGTACATCGAGGCCGGTTGGTGGAATAGATGCAGCTTCCATTCACCCCACCATATGTCAAAGTTT[T/C,A]
TGCTCTTGAATCCCGCCAGCTCGATATTCTCAATGCTGCCCAGAGGAGGTCCTTGGAGATTGAGCAGTCGATCCATCATCAAGGTTGATGAAATTTCCCC

Reverse complement sequence

GGGGAAATTTCATCAACCTTGATGATGGATCGACTGCTCAATCTCCAAGGACCTCCTCTGGGCAGCATTGAGAATATCGAGCTGGCGGGATTCAAGAGCA[A/G,T]
AAACTTTGACATATGGTGGGGTGAATGGAAGCTGCATCTATTCCACCAACCGGCCTCGATGTACATGACAGATCTCTTCCCTGATGTTGTACCTCAGGTA

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 96.60% 2.10% 0.89% 0.36% C: 0.02%
All Indica  2759 98.80% 0.10% 0.51% 0.62% C: 0.04%
All Japonica  1512 92.30% 6.00% 1.79% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.90% 0.20% 0.22% 0.65% NA
Indica III  913 97.70% 0.00% 1.10% 1.10% C: 0.11%
Indica Intermediate  786 99.00% 0.10% 0.38% 0.51% NA
Temperate Japonica  767 85.30% 11.50% 3.26% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg0115667573 T -> A LOC_Os01g28020.1 missense_variant ; p.Lys294Ile; MODERATE nonsynonymous_codon ; K294I Average:37.916; most accessible tissue: Minghui63 flag leaf, score: 48.324 probably damaging 2.61 DELETERIOUS 0.01
vg0115667573 T -> DEL LOC_Os01g28020.1 N frameshift_variant Average:37.916; most accessible tissue: Minghui63 flag leaf, score: 48.324 N N N N
vg0115667573 T -> C LOC_Os01g28020.1 missense_variant ; p.Lys294Arg; MODERATE nonsynonymous_codon ; K294R Average:37.916; most accessible tissue: Minghui63 flag leaf, score: 48.324 benign 0.419 TOLERATED 0.49

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0115667573 9.14E-06 9.15E-06 mr1112 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