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Detailed information for vg0714200726:

Variant ID: vg0714200726 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14200726
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTAATGTATCTGTGTTTCAGAGGGCATGGCTAGCAAATCCTGAGGCTAGCCAATATTTAGCATTTTTTTTTTCTGGAATTAACTCATCAGTGACGGGTC[G/A]
GAACAAAAATCCGTCAAAAGTAACCTAACCTGTGACGGACTAGCAAATAAAGGCCCGTCAGAGGTGACCTACCTGTGACGGGCCTTTACTTTTGGGGCCG

Reverse complement sequence

CGGCCCCAAAAGTAAAGGCCCGTCACAGGTAGGTCACCTCTGACGGGCCTTTATTTGCTAGTCCGTCACAGGTTAGGTTACTTTTGACGGATTTTTGTTC[C/T]
GACCCGTCACTGATGAGTTAATTCCAGAAAAAAAAAATGCTAAATATTGGCTAGCCTCAGGATTTGCTAGCCATGCCCTCTGAAACACAGATACATTACA

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 96.50% 0.80% 1.18% 1.50% NA
All Indica  2759 97.20% 1.40% 1.41% 0.00% NA
All Japonica  1512 94.30% 0.00% 0.99% 4.70% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.80% 0.80% 1.34% 0.00% NA
Indica II  465 95.30% 2.40% 2.37% 0.00% NA
Indica III  913 98.70% 0.30% 0.99% 0.00% NA
Indica Intermediate  786 96.20% 2.40% 1.40% 0.00% NA
Temperate Japonica  767 92.20% 0.00% 0.78% 7.04% NA
Tropical Japonica  504 97.20% 0.00% 1.19% 1.59% NA
Japonica Intermediate  241 95.00% 0.00% 1.24% 3.73% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg0714200726 G -> DEL LOC_Os07g24960.1 N frameshift_variant Average:25.379; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N
vg0714200726 G -> A LOC_Os07g24960.1 missense_variant ; p.Arg903Gln; MODERATE nonsynonymous_codon ; R903Q Average:25.379; most accessible tissue: Minghui63 flag leaf, score: 42.036 unknown unknown TOLERATED 0.45

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714200726 7.72E-06 NA mr1123 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