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Detailed information for vg1121758646:

Variant ID: vg1121758646 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21758646
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGCGAAAGTCAGTTAGTTGATTCGGGTCCTCTTTCTTGGACAGGAGGATGATGGAAGCTGTGTTGACGAGATGCAGGTGCTGGGAATTCACTCTCCAG[G/C]
CTAAGTTAAGGGCCGCAACCAAGTCATCTTTGATAATTCCCCAACAAACCTTGAAAAAGGTGGCGCTAAAACCATCTGGCTCTGGCGCCTTGTCACTTGG

Reverse complement sequence

CCAAGTGACAAGGCGCCAGAGCCAGATGGTTTTAGCGCCACCTTTTTCAAGGTTTGTTGGGGAATTATCAAAGATGACTTGGTTGCGGCCCTTAACTTAG[C/G]
CTGGAGAGTGAATTCCCAGCACCTGCATCTCGTCAACACAGCTTCCATCATCCTCCTGTCCAAGAAAGAGGACCCGAATCAACTAACTGACTTTCGCCCA

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 41.30% 37.50% 3.83% 17.39% NA
All Indica  2759 25.70% 59.60% 4.28% 10.40% NA
All Japonica  1512 65.40% 2.20% 1.85% 30.56% NA
Aus  269 77.30% 16.70% 3.35% 2.60% NA
Indica I  595 7.90% 79.50% 6.22% 6.39% NA
Indica II  465 14.60% 71.60% 4.09% 9.68% NA
Indica III  913 42.40% 40.10% 2.19% 15.33% NA
Indica Intermediate  786 26.30% 60.20% 5.34% 8.14% NA
Temperate Japonica  767 76.90% 2.30% 2.09% 18.64% NA
Tropical Japonica  504 53.40% 2.00% 1.19% 43.45% NA
Japonica Intermediate  241 53.90% 2.10% 2.49% 41.49% NA
VI/Aromatic  96 15.60% 17.70% 23.96% 42.71% NA
Intermediate  90 32.20% 36.70% 3.33% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121758646 G -> DEL LOC_Os11g36880.1 N frameshift_variant Average:34.823; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg1121758646 G -> C LOC_Os11g36880.1 missense_variant ; p.Ala377Gly; MODERATE nonsynonymous_codon ; A377G Average:34.823; most accessible tissue: Minghui63 root, score: 45.031 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121758646 9.27E-06 9.27E-06 mr1249 Ind_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
vg1121758646 NA 7.58E-06 mr1283_2 Ind_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
vg1121758646 NA 1.88E-07 mr1624_2 Ind_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
vg1121758646 NA 3.13E-08 mr1740_2 Ind_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
vg1121758646 NA 8.08E-06 mr1849_2 Ind_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
vg1121758646 NA 4.07E-06 mr1873_2 Ind_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
vg1121758646 NA 1.85E-06 mr1908_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
vg1121758646 NA 1.35E-06 mr1924_2 Ind_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
vg1121758646 NA 1.53E-06 mr1943_2 Ind_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