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Detailed information for vg1220731451:

Variant ID: vg1220731451 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20731451
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAGGATATACCTCATCTACCCACCGTCAGCAAGTTGAGGTTAGATGTGAACACATGGTGGCATGGCCATACCATTGGTGTAACCCTTGCAAGAATCATC[T/G]
AAAGGTGTAACAACATCGAAAACATCTCCATTCGCGTCCGTGGCTTGGTAAGCTTGATCACTTAGCATATTTAATTTGTATTCATTCACTTCCTTTTAAG

Reverse complement sequence

CTTAAAAGGAAGTGAATGAATACAAATTAAATATGCTAAGTGATCAAGCTTACCAAGCCACGGACGCGAATGGAGATGTTTTCGATGTTGTTACACCTTT[A/C]
GATGATTCTTGCAAGGGTTACACCAATGGTATGGCCATGCCACCATGTGTTCACATCTAACCTCAACTTGCTGACGGTGGGTAGATGAGGTATATCCTTC

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 78.20% 21.60% 0.17% 0.00% NA
All Indica  2759 97.80% 2.00% 0.22% 0.00% NA
All Japonica  1512 39.00% 60.90% 0.13% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 97.30% 2.20% 0.50% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 99.00% 0.90% 0.11% 0.00% NA
Indica Intermediate  786 97.80% 1.90% 0.25% 0.00% NA
Temperate Japonica  767 9.80% 90.20% 0.00% 0.00% NA
Tropical Japonica  504 78.00% 21.80% 0.20% 0.00% NA
Japonica Intermediate  241 50.20% 49.40% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220731451 T -> G LOC_Os12g34200.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:38.499; most accessible tissue: Callus, score: 80.206 N N N N
vg1220731451 T -> G LOC_Os12g34210.1 upstream_gene_variant ; 1633.0bp to feature; MODIFIER silent_mutation Average:38.499; most accessible tissue: Callus, score: 80.206 N N N N
vg1220731451 T -> G LOC_Os12g34190.1 downstream_gene_variant ; 4063.0bp to feature; MODIFIER silent_mutation Average:38.499; most accessible tissue: Callus, score: 80.206 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220731451 NA 2.02E-06 mr1013 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
vg1220731451 NA 2.59E-35 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
vg1220731451 NA 1.23E-33 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
vg1220731451 NA 5.84E-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
vg1220731451 NA 7.87E-06 mr1157 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
vg1220731451 NA 6.28E-06 mr1179 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
vg1220731451 NA 5.27E-06 mr1328 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
vg1220731451 6.18E-55 2.11E-162 mr1334 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
vg1220731451 6.98E-21 8.57E-35 mr1334 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
vg1220731451 NA 9.03E-06 mr1446 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
vg1220731451 NA 2.19E-06 mr1577 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
vg1220731451 NA 1.20E-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
vg1220731451 NA 8.41E-08 mr1864 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
vg1220731451 NA 1.08E-46 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
vg1220731451 9.21E-69 2.98E-190 mr1334_2 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
vg1220731451 3.62E-21 5.97E-43 mr1334_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
vg1220731451 NA 6.62E-60 mr1390_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
vg1220731451 NA 2.11E-61 mr1490_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
vg1220731451 4.58E-23 2.30E-75 mr1991_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
vg1220731451 1.12E-14 2.68E-20 mr1991_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