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Detailed information for vg1214801425:

Variant ID: vg1214801425 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14801425
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCAATATTTTGTTCTAGGGACACATGTTTTAAAGTAAGCAGCCGAAATTCCTTCATCAATTCTTGGCACTTCTCATTATAAACCATTAATATCATTCTT[G/A]
CATTCATATTCTCCTGCCAATTGATTGATTACCAGCAAAGAATCCCCCATGATTTCAATAGCATTGGCTTCAACTTCCTTGAGTAATCGCAACCCTTTAA

Reverse complement sequence

TTAAAGGGTTGCGATTACTCAAGGAAGTTGAAGCCAATGCTATTGAAATCATGGGGGATTCTTTGCTGGTAATCAATCAATTGGCAGGAGAATATGAATG[C/T]
AAGAATGATATTAATGGTTTATAATGAGAAGTGCCAAGAATTGATGAAGGAATTTCGGCTGCTTACTTTAAAACATGTGTCCCTAGAACAAAATATTGAA

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 43.50% 0.10% 30.15% 26.24% NA
All Indica  2759 33.00% 0.20% 43.13% 23.67% NA
All Japonica  1512 68.60% 0.00% 2.18% 29.23% NA
Aus  269 19.30% 0.00% 60.59% 20.07% NA
Indica I  595 36.00% 0.20% 36.81% 27.06% NA
Indica II  465 36.10% 0.20% 43.23% 20.43% NA
Indica III  913 27.70% 0.20% 46.11% 25.96% NA
Indica Intermediate  786 35.00% 0.30% 44.40% 20.36% NA
Temperate Japonica  767 89.20% 0.00% 1.17% 9.65% NA
Tropical Japonica  504 42.30% 0.00% 3.37% 54.37% NA
Japonica Intermediate  241 58.10% 0.00% 2.90% 39.00% NA
VI/Aromatic  96 13.50% 0.00% 19.79% 66.67% NA
Intermediate  90 47.80% 0.00% 22.22% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214801425 G -> DEL N N silent_mutation Average:10.428; most accessible tissue: Callus, score: 43.476 N N N N
vg1214801425 G -> A LOC_Os12g25570.1 downstream_gene_variant ; 1770.0bp to feature; MODIFIER silent_mutation Average:10.428; most accessible tissue: Callus, score: 43.476 N N N N
vg1214801425 G -> A LOC_Os12g25580.1 intron_variant ; MODIFIER silent_mutation Average:10.428; most accessible tissue: Callus, score: 43.476 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214801425 NA 1.29E-08 mr1005 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
vg1214801425 NA 5.59E-36 mr1017 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
vg1214801425 NA 2.56E-30 mr1022 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
vg1214801425 NA 8.96E-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
vg1214801425 NA 6.66E-35 mr1055 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
vg1214801425 NA 4.90E-47 mr1079 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
vg1214801425 1.81E-06 1.82E-06 mr1085 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
vg1214801425 NA 2.42E-06 mr1086 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
vg1214801425 NA 8.68E-08 mr1088 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
vg1214801425 NA 7.99E-08 mr1104 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
vg1214801425 8.18E-06 4.60E-07 mr1139 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
vg1214801425 NA 8.85E-63 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
vg1214801425 NA 3.85E-07 mr1155 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
vg1214801425 NA 2.07E-15 mr1156 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
vg1214801425 NA 4.10E-07 mr1156 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
vg1214801425 NA 2.02E-07 mr1213 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
vg1214801425 NA 5.20E-08 mr1224 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
vg1214801425 2.97E-06 3.17E-09 mr1225 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
vg1214801425 NA 2.74E-07 mr1229 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
vg1214801425 NA 2.68E-07 mr1246 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
vg1214801425 NA 2.78E-53 mr1390 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
vg1214801425 NA 1.00E-06 mr1404 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
vg1214801425 NA 2.36E-07 mr1437 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
vg1214801425 NA 2.17E-52 mr1490 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
vg1214801425 NA 1.84E-63 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
vg1214801425 NA 8.27E-07 mr1620 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
vg1214801425 NA 6.08E-06 mr1763 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
vg1214801425 NA 2.34E-10 mr1790 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
vg1214801425 NA 3.53E-14 mr1982 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
vg1214801425 NA 2.13E-06 mr1020_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
vg1214801425 NA 2.95E-39 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
vg1214801425 NA 5.01E-48 mr1055_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
vg1214801425 NA 2.35E-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
vg1214801425 NA 9.23E-08 mr1749_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
vg1214801425 NA 2.81E-14 mr1790_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
vg1214801425 NA 2.02E-08 mr1821_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
vg1214801425 NA 1.76E-06 mr1905_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