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Detailed information for vg1218479048:

Variant ID: vg1218479048 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18479048
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AAACATCACATCTTTATCAAACTTAGCAACCAAACAAGTTATCACAGGTGAAACAGAATTTTCAAAATCAGCTTTAAACACTCTTCCATAACGAGAAATA[T/G]
TCAGCACAGAATCACCACAAGAATCAAAAATTTTACTTCTAGTTTTCTTAAAGTGAACTTCAAACTCTTCATCAACAATTTGTGAAACCGAAAGCAAATT

Reverse complement sequence

AATTTGCTTTCGGTTTCACAAATTGTTGATGAAGAGTTTGAAGTTCACTTTAAGAAAACTAGAAGTAAAATTTTTGATTCTTGTGGTGATTCTGTGCTGA[A/C]
TATTTCTCGTTATGGAAGAGTGTTTAAAGCTGATTTTGAAAATTCTGTTTCACCTGTGATAACTTGTTTGGTTGCTAAGTTTGATAAAGATGTGATGTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 16.30% 4.60% 51.29% 27.85% NA
All Indica  2759 5.90% 6.30% 69.23% 18.63% NA
All Japonica  1512 36.20% 1.50% 14.62% 47.75% NA
Aus  269 8.90% 7.10% 78.44% 5.58% NA
Indica I  595 7.60% 4.90% 77.82% 9.75% NA
Indica II  465 5.20% 6.50% 74.41% 13.98% NA
Indica III  913 5.40% 6.70% 62.43% 25.52% NA
Indica Intermediate  786 5.60% 6.70% 67.56% 20.10% NA
Temperate Japonica  767 60.20% 0.40% 5.87% 33.51% NA
Tropical Japonica  504 5.00% 2.80% 20.24% 72.02% NA
Japonica Intermediate  241 24.90% 2.10% 30.71% 42.32% NA
VI/Aromatic  96 8.30% 1.00% 41.67% 48.96% NA
Intermediate  90 30.00% 3.30% 46.67% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218479048 T -> DEL LOC_Os12g30770.1 N frameshift_variant Average:7.856; most accessible tissue: Minghui63 flag leaf, score: 12.43 N N N N
vg1218479048 T -> G LOC_Os12g30770.1 missense_variant ; p.Asn89Thr; MODERATE nonsynonymous_codon Average:7.856; most accessible tissue: Minghui63 flag leaf, score: 12.43 benign 1.255 DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218479048 2.54E-06 NA mr1745 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