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Detailed information for vg1203268826:

Variant ID: vg1203268826 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3268826
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGGACCTCTTTGACAGCCATCACAGCCTTGCCCGTGCGGTCATTTCTGAATTTTCTCCACGTCATGGGAGCTTGACTTGGCCTTGGCGGCTGTCCCTG[A/G]
TTCGCCAGCTGAGGTTGGCGAACGGTGAGAGGAGTCGGTTCGGCGACCTGTGCTTGTACTTGGGCTTGGGCAGTGGCGATGGAGGCTTTATCGTACTCGG

Reverse complement sequence

CCGAGTACGATAAAGCCTCCATCGCCACTGCCCAAGCCCAAGTACAAGCACAGGTCGCCGAACCGACTCCTCTCACCGTTCGCCAACCTCAGCTGGCGAA[T/C]
CAGGGACAGCCGCCAAGGCCAAGTCAAGCTCCCATGACGTGGAGAAAATTCAGAAATGACCGCACGGGCAAGGCTGTGATGGCTGTCAAAGAGGTCCAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 35.80% 13.90% 8.65% 41.60% NA
All Indica  2759 5.80% 19.20% 12.69% 62.38% NA
All Japonica  1512 93.10% 1.30% 2.31% 3.31% NA
Aus  269 5.90% 33.10% 5.58% 55.39% NA
Indica I  595 4.20% 7.90% 6.39% 81.51% NA
Indica II  465 4.70% 8.60% 19.78% 66.88% NA
Indica III  913 6.40% 33.20% 13.03% 47.43% NA
Indica Intermediate  786 6.90% 17.70% 12.85% 62.60% NA
Temperate Japonica  767 95.60% 0.30% 3.13% 1.04% NA
Tropical Japonica  504 87.90% 3.00% 1.59% 7.54% NA
Japonica Intermediate  241 96.30% 0.80% 1.24% 1.66% NA
VI/Aromatic  96 62.50% 6.20% 2.08% 29.17% NA
Intermediate  90 55.60% 16.70% 7.78% 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
vg1203268826 A -> DEL LOC_Os12g06720.1 N frameshift_variant Average:9.281; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N
vg1203268826 A -> G LOC_Os12g06720.1 synonymous_variant ; p.Asn615Asn; LOW synonymous_codon Average:9.281; most accessible tissue: Zhenshan97 panicle, score: 16.188 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203268826 4.64E-06 NA mr1639 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
vg1203268826 NA 3.53E-06 mr1639 Ind_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