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Detailed information for vg1224819316:

Variant ID: vg1224819316 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24819316
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAGCAACCTTTTCGACGCTGACACGCCATGTTTCGCCACTGGGTGCTTTCAGGTTGAACCCTTTGGTGATCTGACCACTGAATCTGTCCGCAACTTTC[T/C]
CCGGTATGCTCTGAGATGAAAACAATAATCTGGTTAACTTCGTTAGATGATACTCCAACTATAGTTGGCATGTTGAATGTTGTGTCCAGATAACAGTGAC

Reverse complement sequence

GTCACTGTTATCTGGACACAACATTCAACATGCCAACTATAGTTGGAGTATCATCTAACGAAGTTAACCAGATTATTGTTTTCATCTCAGAGCATACCGG[A/G]
GAAAGTTGCGGACAGATTCAGTGGTCAGATCACCAAAGGGTTCAACCTGAAAGCACCCAGTGGCGAAACATGGCGTGTCAGCGTCGAAAAGGTTGCTGAT

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 89.90% 9.90% 0.00% 0.15% NA
All Indica  2759 93.10% 6.70% 0.00% 0.18% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 2.60% 96.70% 0.00% 0.74% NA
Indica I  595 77.80% 22.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.60% 2.20% 0.00% 0.22% NA
Indica Intermediate  786 95.40% 4.20% 0.00% 0.38% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1224819316 T -> C LOC_Os12g40120.1 missense_variant ; p.Glu44Gly; MODERATE nonsynonymous_codon ; E44G Average:50.201; most accessible tissue: Zhenshan97 panicle, score: 74.671 unknown unknown DELETERIOUS 0.02
vg1224819316 T -> DEL LOC_Os12g40120.1 N frameshift_variant Average:50.201; most accessible tissue: Zhenshan97 panicle, score: 74.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224819316 NA 5.98E-15 mr1158 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
vg1224819316 NA 3.21E-10 mr1730 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
vg1224819316 NA 3.80E-06 mr1344_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
vg1224819316 NA 3.64E-16 mr1587_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