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Detailed information for vg0601268839:

Variant ID: vg0601268839 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1268839
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCGCTTCGGCGGGAGGATCTTTCGACGTGGAGTCATCTTGGGTTACAGCCACTGCGTTCTCGTTTCTGGTCCTAGACGGCCCAGCTGAGATCGGCGTC[G/A]
TGGTGTAAACCGGAAAGACAATCTCGCTGACTTGAGTCGACGCAAGCGTCGTTGAGGCAGGAAGCCCGTAGTTAAGGTTGGCGTTGGCGCTGTTGTCGAC

Reverse complement sequence

GTCGACAACAGCGCCAACGCCAACCTTAACTACGGGCTTCCTGCCTCAACGACGCTTGCGTCGACTCAAGTCAGCGAGATTGTCTTTCCGGTTTACACCA[C/T]
GACGCCGATCTCAGCTGGGCCGTCTAGGACCAGAAACGAGAACGCAGTGGCTGTAACCCAAGATGACTCCACGTCGAAAGATCCTCCCGCCGAAGCGGAG

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 91.70% 8.30% 0.00% 0.00% NA
All Indica  2759 89.90% 10.10% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 95.10% 4.90% 0.00% 0.00% NA
Indica III  913 81.80% 18.20% 0.00% 0.00% NA
Indica Intermediate  786 91.70% 8.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 51.00% 49.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 0.00% 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
vg0601268839 G -> A LOC_Os06g03320.1 missense_variant ; p.Thr80Met; MODERATE nonsynonymous_codon ; T80M Average:48.891; most accessible tissue: Minghui63 young leaf, score: 72.408 probably damaging 2.771 DELETERIOUS 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601268839 4.38E-06 4.38E-06 mr1240 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