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Detailed information for vg0308977626:

Variant ID: vg0308977626 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8977626
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGTGCACGATTCCCGAGGCGCAACTGGGTGGTTACAAGGGAACATGATATATCAATTAACAAAGGAAGGATCAAATGCAACAAATTAGGTAGGTCCGC[T/C]
AATCTGCCTTGCAGACGGGACAACAGATTAAGTGCGACCCTATCAATGCATAATATTTTTCAAGCAACATAATTAAATTTCAAATATAGGCTCAAGATGT

Reverse complement sequence

ACATCTTGAGCCTATATTTGAAATTTAATTATGTTGCTTGAAAAATATTATGCATTGATAGGGTCGCACTTAATCTGTTGTCCCGTCTGCAAGGCAGATT[A/G]
GCGGACCTACCTAATTTGTTGCATTTGATCCTTCCTTTGTTAATTGATATATCATGTTCCCTTGTAACCACCCAGTTGCGCCTCGGGAATCGTGCACTCT

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 58.60% 3.20% 15.87% 22.30% NA
All Indica  2759 43.10% 1.00% 22.15% 33.82% NA
All Japonica  1512 91.10% 7.90% 0.33% 0.66% NA
Aus  269 24.90% 0.70% 42.38% 31.97% NA
Indica I  595 70.90% 0.00% 7.73% 21.34% NA
Indica II  465 30.50% 1.50% 17.42% 50.54% NA
Indica III  913 36.30% 1.20% 34.39% 28.15% NA
Indica Intermediate  786 37.30% 1.10% 21.63% 39.95% NA
Temperate Japonica  767 86.70% 12.30% 0.13% 0.91% NA
Tropical Japonica  504 95.40% 3.80% 0.60% 0.20% NA
Japonica Intermediate  241 95.90% 2.90% 0.41% 0.83% NA
VI/Aromatic  96 83.30% 0.00% 10.42% 6.25% NA
Intermediate  90 63.30% 4.40% 11.11% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0308977626 T -> C LOC_Os03g16280.1 downstream_gene_variant ; 3055.0bp to feature; MODIFIER silent_mutation Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0308977626 T -> C LOC_Os03g16280-LOC_Os03g16290 intergenic_region ; MODIFIER silent_mutation Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0308977626 T -> DEL N N silent_mutation Average:18.891; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308977626 3.42E-06 3.42E-06 mr1396 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