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Detailed information for vg1122373396:

Variant ID: vg1122373396 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22373396
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCACTCAAATAATAAAATCAGACCTTGCACAGGCACTTTCACACTTTGGTGAGCTAAACTCAGATTTTTAGATAATGGAATATAATATCCCGGCCTTT[A/G]
CTCAAAAAGAACTACAGCCAATTATTACAAAGATCCACTCCAGAAGAGAGTGTAGTTCAAGACAAGTTGAACACACCAAACAAGAGAAGAGAGGACCCAA

Reverse complement sequence

TTGGGTCCTCTCTTCTCTTGTTTGGTGTGTTCAACTTGTCTTGAACTACACTCTCTTCTGGAGTGGATCTTTGTAATAATTGGCTGTAGTTCTTTTTGAG[T/C]
AAAGGCCGGGATATTATATTCCATTATCTAAAAATCTGAGTTTAGCTCACCAAAGTGTGAAAGTGCCTGTGCAAGGTCTGATTTTATTATTTGAGTGAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.50% 14.00% 1.69% 55.80% NA
All Indica  2759 19.60% 4.20% 2.07% 74.12% NA
All Japonica  1512 47.90% 29.10% 0.53% 22.42% NA
Aus  269 19.00% 4.10% 3.35% 73.61% NA
Indica I  595 37.10% 5.90% 1.01% 55.97% NA
Indica II  465 22.40% 1.70% 2.37% 73.55% NA
Indica III  913 3.80% 5.00% 2.85% 88.28% NA
Indica Intermediate  786 22.90% 3.60% 1.78% 71.76% NA
Temperate Japonica  767 71.20% 14.20% 0.65% 13.95% NA
Tropical Japonica  504 19.80% 48.60% 0.40% 31.15% NA
Japonica Intermediate  241 32.80% 35.70% 0.41% 31.12% NA
VI/Aromatic  96 3.10% 77.10% 2.08% 17.71% NA
Intermediate  90 28.90% 24.40% 4.44% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122373396 A -> DEL N N silent_mutation Average:14.906; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1122373396 A -> G LOC_Os11g37780.1 downstream_gene_variant ; 2704.0bp to feature; MODIFIER silent_mutation Average:14.906; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg1122373396 A -> G LOC_Os11g37780-LOC_Os11g37790 intergenic_region ; MODIFIER silent_mutation Average:14.906; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122373396 NA 4.79E-07 mr1045 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
vg1122373396 2.92E-07 2.92E-07 mr1060 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
vg1122373396 NA 8.95E-06 mr1126 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
vg1122373396 NA 4.12E-06 mr1192 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
vg1122373396 NA 9.05E-06 mr1287 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
vg1122373396 NA 2.87E-07 mr1521 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
vg1122373396 NA 8.35E-07 mr1596 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
vg1122373396 NA 2.05E-06 mr1614 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
vg1122373396 NA 1.48E-07 mr1617 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
vg1122373396 NA 7.20E-06 mr1740 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
vg1122373396 NA 7.15E-06 mr1741 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
vg1122373396 NA 5.59E-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
vg1122373396 4.72E-06 4.71E-06 mr1797 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
vg1122373396 4.72E-06 4.71E-06 mr1801 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
vg1122373396 NA 3.51E-06 mr1912 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
vg1122373396 3.54E-06 3.54E-06 mr1992 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