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Detailed information for vg1216469080:

Variant ID: vg1216469080 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16469080
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGATAGATAGATAGATAGGATGAATGGAAGATAGTCAAACAGACTTTAGATAGATAGATAGATAGATGAATTACTCGCCACCATAGTTTCTATAAGCAC[A/G]
CTTTCATAGTATAAATACATGTGACCCCAATGAGGAACTCCAACACATCCCATGCATACAACATTTTGACCTTTTTATTTAAGAATTAGAGTAGAGTTAA

Reverse complement sequence

TTAACTCTACTCTAATTCTTAAATAAAAAGGTCAAAATGTTGTATGCATGGGATGTGTTGGAGTTCCTCATTGGGGTCACATGTATTTATACTATGAAAG[T/C]
GTGCTTATAGAAACTATGGTGGCGAGTAATTCATCTATCTATCTATCTATCTAAAGTCTGTTTGACTATCTTCCATTCATCCTATCTATCTATCTATCTA

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 66.50% 18.90% 0.17% 14.37% NA
All Indica  2759 83.70% 2.70% 0.04% 13.59% NA
All Japonica  1512 35.50% 52.60% 0.46% 11.38% NA
Aus  269 72.50% 1.10% 0.00% 26.39% NA
Indica I  595 93.10% 2.70% 0.00% 4.20% NA
Indica II  465 85.80% 4.50% 0.00% 9.68% NA
Indica III  913 77.70% 0.20% 0.11% 22.02% NA
Indica Intermediate  786 82.30% 4.50% 0.00% 13.23% NA
Temperate Japonica  767 8.70% 84.00% 0.26% 7.04% NA
Tropical Japonica  504 82.30% 4.60% 0.60% 12.50% NA
Japonica Intermediate  241 22.80% 53.50% 0.83% 22.82% NA
VI/Aromatic  96 42.70% 1.00% 0.00% 56.25% NA
Intermediate  90 68.90% 23.30% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216469080 A -> DEL N N silent_mutation Average:45.289; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg1216469080 A -> G LOC_Os12g27940.1 upstream_gene_variant ; 39.0bp to feature; MODIFIER silent_mutation Average:45.289; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg1216469080 A -> G LOC_Os12g27930-LOC_Os12g27940 intergenic_region ; MODIFIER silent_mutation Average:45.289; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216469080 NA 3.37E-07 mr1002 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
vg1216469080 1.01E-06 4.93E-61 mr1023 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
vg1216469080 8.55E-06 6.44E-61 mr1142 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
vg1216469080 NA 7.32E-10 mr1282 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
vg1216469080 NA 9.81E-19 mr1308 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
vg1216469080 NA 1.81E-07 mr1308 Jap_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
vg1216469080 NA 8.33E-08 mr1364 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
vg1216469080 NA 4.67E-06 mr1364 Jap_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
vg1216469080 NA 8.53E-17 mr1401 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
vg1216469080 NA 6.43E-09 mr1401 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
vg1216469080 2.31E-06 NA mr1489 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
vg1216469080 7.17E-07 1.12E-62 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
vg1216469080 NA 5.51E-06 mr1578 Jap_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
vg1216469080 NA 4.51E-07 mr1584 Jap_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
vg1216469080 NA 2.12E-07 mr1606 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
vg1216469080 NA 4.07E-09 mr1658 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
vg1216469080 NA 1.57E-13 mr1667 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
vg1216469080 4.86E-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
vg1216469080 NA 4.92E-09 mr1866 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
vg1216469080 NA 3.96E-08 mr1942 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
vg1216469080 NA 2.13E-09 mr1942 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
vg1216469080 NA 2.46E-09 mr1959 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
vg1216469080 1.22E-06 1.03E-74 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
vg1216469080 9.56E-07 1.03E-55 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
vg1216469080 6.27E-06 NA mr1178_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
vg1216469080 NA 1.37E-12 mr1182_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
vg1216469080 9.92E-10 3.35E-80 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
vg1216469080 NA 2.46E-15 mr1489_2 Jap_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
vg1216469080 2.85E-08 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
vg1216469080 NA 1.09E-13 mr1778_2 Jap_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