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Detailed information for vg0109411370:

Variant ID: vg0109411370 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9411370
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATTTTGCTGAACTAGCAGTCAGCAGCTAGAATTACCTGATATGGGCACTAGATGCCAAAATCATGCTTGGTGCTAAGAAACTCCTGAACTGCATTCAG[G/A]
ACCCAACTATTGCAACATCAGCTGGAGGAGTTAATAATTTACCAACTTCAGCCGAGAAAAATCAGGCACTGCATTTCCTGAGGCACCATTTGAATACTAC

Reverse complement sequence

GTAGTATTCAAATGGTGCCTCAGGAAATGCAGTGCCTGATTTTTCTCGGCTGAAGTTGGTAAATTATTAACTCCTCCAGCTGATGTTGCAATAGTTGGGT[C/T]
CTGAATGCAGTTCAGGAGTTTCTTAGCACCAAGCATGATTTTGGCATCTAGTGCCCATATCAGGTAATTCTAGCTGCTGACTGCTAGTTCAGCAAAATCT

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 95.90% 3.40% 0.72% 0.00% NA
All Indica  2759 93.20% 5.60% 1.20% 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 99.00% 0.00% 1.01% 0.00% NA
Indica II  465 85.80% 12.30% 1.94% 0.00% NA
Indica III  913 96.90% 2.80% 0.22% 0.00% NA
Indica Intermediate  786 88.80% 9.20% 2.04% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0109411370 G -> A LOC_Os01g16570.1 missense_variant ; p.Asp13Asn; MODERATE nonsynonymous_codon ; D13N Average:16.382; most accessible tissue: Zhenshan97 root, score: 23.888 unknown unknown TOLERATED 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109411370 6.78E-06 2.19E-07 mr1697 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
vg0109411370 4.06E-06 1.50E-06 mr1697 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