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Detailed information for vg1207089520:

Variant ID: vg1207089520 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7089520
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTATGTTGTTCGATCTCATGTAAATAGCGTTAATAATTAGTACAGATAATTTTGACAACATAAATTATTCCTTCGTATATTACCCATAAACATGCATA[G/C]
GTGAATTAGATATATAATATAAGAAAAACAATCAAAGCCCATATTATGTTTGCGAAAGATGGTGATTGGCAAGTTTACATATAACTGAGACAAAGTGATT

Reverse complement sequence

AATCACTTTGTCTCAGTTATATGTAAACTTGCCAATCACCATCTTTCGCAAACATAATATGGGCTTTGATTGTTTTTCTTATATTATATATCTAATTCAC[C/G]
TATGCATGTTTATGGGTAATATACGAAGGAATAATTTATGTTGTCAAAATTATCTGTACTAATTATTAACGCTATTTACATGAGATCGAACAACATAATA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 4.30% 1.04% 12.61% NA
All Indica  2759 99.10% 0.30% 0.11% 0.54% NA
All Japonica  1512 50.20% 11.60% 1.59% 36.57% NA
Aus  269 85.10% 5.20% 7.43% 2.23% NA
Indica I  595 99.30% 0.00% 0.17% 0.50% NA
Indica II  465 98.30% 0.40% 0.00% 1.29% NA
Indica III  913 99.70% 0.10% 0.11% 0.11% NA
Indica Intermediate  786 98.70% 0.50% 0.13% 0.64% NA
Temperate Japonica  767 44.60% 1.00% 2.22% 52.15% NA
Tropical Japonica  504 53.20% 30.00% 0.79% 16.07% NA
Japonica Intermediate  241 61.80% 7.10% 1.24% 29.88% NA
VI/Aromatic  96 93.80% 0.00% 0.00% 6.25% NA
Intermediate  90 71.10% 8.90% 2.22% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1207089520 G -> C LOC_Os12g12840-LOC_Os12g12850 intergenic_region ; MODIFIER silent_mutation Average:60.073; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg1207089520 G -> DEL N N silent_mutation Average:60.073; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207089520 NA 7.80E-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
vg1207089520 NA 8.79E-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
vg1207089520 NA 2.38E-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
vg1207089520 NA 1.15E-06 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
vg1207089520 NA 4.68E-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
vg1207089520 NA 1.66E-08 mr1648 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
vg1207089520 NA 1.09E-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
vg1207089520 NA 2.17E-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
vg1207089520 9.70E-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
vg1207089520 2.82E-06 NA mr1960 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
vg1207089520 NA 4.10E-08 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
vg1207089520 NA 8.61E-06 mr1072_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
vg1207089520 4.70E-06 NA mr1082_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
vg1207089520 NA 9.62E-09 mr1543_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
vg1207089520 NA 7.52E-08 mr1642_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
vg1207089520 NA 2.39E-07 mr1808_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
vg1207089520 NA 3.70E-07 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