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Detailed information for vg0122974648:

Variant ID: vg0122974648 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22974648
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTATTTAAAATGAAATTTGTAATGGTACGAATCAAATTAATCCAAATACTTATAATTTTAGATATTTTAGCATAGTTTAATATTTTTTTAAAAAAGTA[C/A]
TTGAGTGGAGTGGTAGTTAGAGGGTATAACAAGGATAAATTTAAATGGGTGATGGATGGGACAAATAGTATTTTAGAGTAACTAAGTATTTTGAAACATT

Reverse complement sequence

AATGTTTCAAAATACTTAGTTACTCTAAAATACTATTTGTCCCATCCATCACCCATTTAAATTTATCCTTGTTATACCCTCTAACTACCACTCCACTCAA[G/T]
TACTTTTTTAAAAAAATATTAAACTATGCTAAAATATCTAAAATTATAAGTATTTGGATTAATTTGATTCGTACCATTACAAATTTCATTTTAAATAAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 1.20% 1.57% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 91.40% 3.80% 4.83% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 86.70% 5.20% 8.08% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 3.70% 4.56% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0122974648 C -> A LOC_Os01g40630-LOC_Os01g40640 intergenic_region ; MODIFIER silent_mutation Average:64.621; most accessible tissue: Minghui63 flower, score: 78.426 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122974648 4.05E-06 4.05E-06 mr1651 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
vg0122974648 NA 8.08E-06 mr1821_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