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Detailed information for vg1216482741:

Variant ID: vg1216482741 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16482741
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATACGGATTACCAGGCAACTGCGTGTGCTTGCGCTGCATGAACGACTTCGTCGTCGTCGGCCAGCAGCTGGCGGAGAACGATCACGGCGAGCTCGGCG[G/T]
CGGCGGCGACGAGCACACGATGTACACGTTCGAGGTGACGGTGACGAACCGGTGCTGCTGCGAGGTGAGCAGCGTCGTCGTGGCGGCGCCGGGGTTCCGG

Reverse complement sequence

CCGGAACCCCGGCGCCGCCACGACGACGCTGCTCACCTCGCAGCAGCACCGGTTCGTCACCGTCACCTCGAACGTGTACATCGTGTGCTCGTCGCCGCCG[C/A]
CGCCGAGCTCGCCGTGATCGTTCTCCGCCAGCTGCTGGCCGACGACGACGAAGTCGTTCATGCAGCGCAAGCACACGCAGTTGCCTGGTAATCCGTATAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.00% 27.00% 0.93% 13.01% NA
All Indica  2759 54.30% 32.10% 0.58% 12.98% NA
All Japonica  1512 70.00% 20.00% 1.46% 8.60% NA
Aus  269 54.30% 17.80% 1.49% 26.39% NA
Indica I  595 67.90% 27.90% 0.17% 4.03% NA
Indica II  465 84.10% 6.20% 0.65% 9.03% NA
Indica III  913 24.20% 54.00% 0.44% 21.36% NA
Indica Intermediate  786 61.50% 25.20% 1.02% 12.34% NA
Temperate Japonica  767 83.70% 9.00% 1.30% 6.00% NA
Tropical Japonica  504 55.20% 34.10% 0.60% 10.12% NA
Japonica Intermediate  241 57.30% 25.30% 3.73% 13.69% NA
VI/Aromatic  96 28.10% 16.70% 2.08% 53.12% NA
Intermediate  90 66.70% 27.80% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216482741 G -> DEL LOC_Os12g27950.1 N frameshift_variant Average:61.97; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg1216482741 G -> T LOC_Os12g27950.1 missense_variant ; p.Gly47Val; MODERATE nonsynonymous_codon ; G47V Average:61.97; most accessible tissue: Zhenshan97 panicle, score: 78.302 unknown unknown TOLERATED 0.28

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216482741 5.10E-06 NA mr1491 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
vg1216482741 5.09E-06 NA mr1778 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
vg1216482741 NA 4.91E-09 mr1002_2 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
vg1216482741 9.21E-06 NA mr1022_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
vg1216482741 3.04E-06 NA mr1023_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
vg1216482741 3.66E-09 NA mr1079_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
vg1216482741 5.36E-08 NA mr1079_2 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
vg1216482741 8.55E-07 NA mr1132_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
vg1216482741 1.36E-08 NA mr1489_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
vg1216482741 NA 8.35E-07 mr1582_2 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
vg1216482741 2.19E-06 NA mr1778_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