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Detailed information for vg0401212486:

Variant ID: vg0401212486 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1212486
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAACGTTGTTAACTGAAGCACAAAATATCTCTTCTGTTCTTACTCATTTGACCCTATTACATATGGGACCCACCCGTCAGTTCTCTCTTCTTCTCTCC[T/C]
CTCTTTTCTTCTCCTCTCCTCTCTTTCACGGATCAGCGGCGAACCGGCACCGATGGGGCGGCGGCTTGCCGCGGCGGCGGCGCTCTGAGGGGGCGGAGGG

Reverse complement sequence

CCCTCCGCCCCCTCAGAGCGCCGCCGCCGCGGCAAGCCGCCGCCCCATCGGTGCCGGTTCGCCGCTGATCCGTGAAAGAGAGGAGAGGAGAAGAAAAGAG[A/G]
GGAGAGAAGAAGAGAGAACTGACGGGTGGGTCCCATATGTAATAGGGTCAAATGAGTAAGAACAGAAGAGATATTTTGTGCTTCAGTTAACAACGTTAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.80% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 83.60% 16.40% 0.00% 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 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 82.10% 17.90% 0.00% 0.00% NA
Tropical Japonica  504 81.90% 18.10% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0401212486 T -> C LOC_Os04g02980.1 intron_variant ; MODIFIER silent_mutation Average:45.223; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401212486 4.70E-07 NA mr1489 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
vg0401212486 1.01E-07 NA mr1778 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
vg0401212486 5.32E-06 NA mr1778_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