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Detailed information for vg1207087743:

Variant ID: vg1207087743 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7087743
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGAAAAAATTTAATCCTTAATGTCAATTTAAATCGGTAGATCCATAATATTAAACCGATGAACCCATTAAATCCACATATATGCACCACTGACTTTTG[C/G]
CATTTGTGTGACAACCAAATAACAACGAAACAACATAGTAATAAATAATAACACACATATAAGTTGGATATTATGCTTTAAGGTGTAAAAACATACTGCA

Reverse complement sequence

TGCAGTATGTTTTTACACCTTAAAGCATAATATCCAACTTATATGTGTGTTATTATTTATTACTATGTTGTTTCGTTGTTATTTGGTTGTCACACAAATG[G/C]
CAAAAGTCAGTGGTGCATATATGTGGATTTAATGGGTTCATCGGTTTAATATTATGGATCTACCGATTTAAATTGACATTAAGGATTAAATTTTTTCCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.20% 8.10% 1.18% 14.54% NA
All Indica  2759 98.40% 0.50% 0.14% 1.01% NA
All Japonica  1512 36.40% 23.30% 1.39% 38.82% NA
Aus  269 73.60% 3.00% 11.15% 12.27% NA
Indica I  595 99.00% 0.20% 0.17% 0.67% NA
Indica II  465 98.10% 0.40% 0.00% 1.51% NA
Indica III  913 99.00% 0.40% 0.11% 0.44% NA
Indica Intermediate  786 97.30% 0.80% 0.25% 1.65% NA
Temperate Japonica  767 40.70% 2.50% 1.56% 55.28% NA
Tropical Japonica  504 20.60% 60.70% 1.59% 17.06% NA
Japonica Intermediate  241 56.00% 11.60% 0.41% 31.95% NA
VI/Aromatic  96 81.20% 0.00% 1.04% 17.71% NA
Intermediate  90 65.60% 10.00% 0.00% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1207087743 C -> DEL N N silent_mutation Average:28.923; most accessible tissue: Minghui63 flower, score: 45.483 N N N N
vg1207087743 C -> G LOC_Os12g12840-LOC_Os12g12850 intergenic_region ; MODIFIER silent_mutation Average:28.923; most accessible tissue: Minghui63 flower, score: 45.483 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207087743 4.72E-07 NA mr1236 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
vg1207087743 NA 7.53E-07 mr1304 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
vg1207087743 NA 1.38E-07 mr1345 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
vg1207087743 NA 7.92E-06 mr1382 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
vg1207087743 NA 3.22E-06 mr1417 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
vg1207087743 NA 3.08E-06 mr1422 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
vg1207087743 NA 9.88E-07 mr1583 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
vg1207087743 NA 7.70E-06 mr1633 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
vg1207087743 NA 1.13E-06 mr1696 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
vg1207087743 NA 3.19E-06 mr1697 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
vg1207087743 NA 7.17E-06 mr1876 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
vg1207087743 5.83E-06 NA mr1906 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
vg1207087743 7.65E-07 NA mr1960 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
vg1207087743 NA 3.53E-07 mr1047_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
vg1207087743 NA 1.46E-06 mr1815_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