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Detailed information for vg1218421558:

Variant ID: vg1218421558 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18421558
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCCTCCGTCGCCACCGCTCAAGCTCAAGCACAAGTTCAAGTTGCCGAACCACCTCCCCTCTCTGTTCGCCAGTCTCAGTCGGCGATCCAAGGACAGCC[G/A]
CCAAGGCAAGGCCAGGCCCCCCATAACTTGGAGAAAGTTCAGAACAGACCGTGCGGGCAAAGCTGTGATGGCGGTCGAAGAAGTGCAAGCCCTCCGCAAG

Reverse complement sequence

CTTGCGGAGGGCTTGCACTTCTTCGACCGCCATCACAGCTTTGCCCGCACGGTCTGTTCTGAACTTTCTCCAAGTTATGGGGGGCCTGGCCTTGCCTTGG[C/T]
GGCTGTCCTTGGATCGCCGACTGAGACTGGCGAACAGAGAGGGGAGGTGGTTCGGCAACTTGAACTTGTGCTTGAGCTTGAGCGGTGGCGACGGAGGCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.30% 2.20% 2.37% 4.13% NA
All Indica  2759 88.00% 1.00% 3.99% 7.00% NA
All Japonica  1512 95.10% 4.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 68.70% 1.30% 9.58% 20.34% NA
Indica II  465 97.00% 0.90% 0.86% 1.29% NA
Indica III  913 95.60% 0.80% 1.97% 1.64% NA
Indica Intermediate  786 88.50% 1.00% 3.94% 6.49% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 79.30% 20.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 1.10% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218421558 G -> DEL LOC_Os12g30670.1 N frameshift_variant Average:33.047; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N
vg1218421558 G -> A LOC_Os12g30670.1 synonymous_variant ; p.Pro317Pro; LOW synonymous_codon Average:33.047; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218421558 2.62E-06 2.62E-06 mr1356 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
vg1218421558 NA 2.34E-06 mr1460 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