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Detailed information for vg0914487465:

Variant ID: vg0914487465 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 14487465
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACAATTACGCCAATTAAATAAAGTTTGATTCCCAGTTAAAAAATAAAAAAGAACAAACCACAAGAGAAATTGAAATGATTCATAAACTAAAATAATGGA[A/C]
TAGAAATAAAATTAAATTATCAGTTGTAGTTTGGCCAAATGTATTCCATATCACAAAATTATGAAACTTTCAAGGGAAGAAAAATAAATTAAGCAATATT

Reverse complement sequence

AATATTGCTTAATTTATTTTTCTTCCCTTGAAAGTTTCATAATTTTGTGATATGGAATACATTTGGCCAAACTACAACTGATAATTTAATTTTATTTCTA[T/G]
TCCATTATTTTAGTTTATGAATCATTTCAATTTCTCTTGTGGTTTGTTCTTTTTTATTTTTTAACTGGGAATCAAACTTTATTTAATTGGCGTAATTGTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.50% 6.10% 1.35% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 77.20% 18.70% 4.10% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 58.40% 35.60% 6.00% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 90.90% 3.70% 5.39% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 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
vg0914487465 A -> C LOC_Os09g24370-LOC_Os09g24390 intergenic_region ; MODIFIER silent_mutation Average:23.022; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0914487465 2.38E-06 NA mr1024_2 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
vg0914487465 NA 4.54E-13 mr1182_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
vg0914487465 NA 5.88E-06 mr1182_2 Jap_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
vg0914487465 NA 8.68E-06 mr1866_2 Jap_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