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Detailed information for vg1124078018:

Variant ID: vg1124078018 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24078018
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACATGAATTTCTGAAGATCGAGCAGCAGGTGGACTAGAGCTGACTGTGTCCTGAACATGGGTAGACACATCACTGCTCTGATTAGATGGTCCAGGAGTG[C/T]
TGTTCCTGAAATTTGCACTCTTCTGCTGTTGCCATAATTTGCTCTTCTCGATGCCACAGTGGCAAAACAAAGCCCAGATGACGGTTACGAACTCGACACC

Reverse complement sequence

GGTGTCGAGTTCGTAACCGTCATCTGGGCTTTGTTTTGCCACTGTGGCATCGAGAAGAGCAAATTATGGCAACAGCAGAAGAGTGCAAATTTCAGGAACA[G/A]
CACTCCTGGACCATCTAATCAGAGCAGTGATGTGTCTACCCATGTTCAGGACACAGTCAGCTCTAGTCCACCTGCTGCTCGATCTTCAGAAATTCATGTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.90% 17.60% 0.89% 43.63% NA
All Indica  2759 32.90% 2.80% 1.30% 62.96% NA
All Japonica  1512 45.90% 40.40% 0.20% 13.49% NA
Aus  269 23.80% 44.60% 1.12% 30.48% NA
Indica I  595 5.00% 2.20% 1.68% 91.09% NA
Indica II  465 27.10% 1.90% 0.22% 70.75% NA
Indica III  913 54.80% 1.10% 1.10% 43.04% NA
Indica Intermediate  786 32.20% 5.70% 1.91% 60.18% NA
Temperate Japonica  767 39.40% 52.90% 0.13% 7.56% NA
Tropical Japonica  504 52.80% 33.30% 0.00% 13.89% NA
Japonica Intermediate  241 52.30% 15.40% 0.83% 31.54% NA
VI/Aromatic  96 86.50% 1.00% 0.00% 12.50% NA
Intermediate  90 44.40% 25.60% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124078018 C -> T LOC_Os11g40390.1 missense_variant ; p.Ser393Asn; MODERATE nonsynonymous_codon ; S393N Average:20.029; most accessible tissue: Callus, score: 86.44 unknown unknown TOLERATED 1.00
vg1124078018 C -> DEL LOC_Os11g40390.1 N frameshift_variant Average:20.029; most accessible tissue: Callus, score: 86.44 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124078018 4.41E-06 NA mr1088_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
vg1124078018 4.45E-06 NA mr1131_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
vg1124078018 2.75E-06 NA mr1199_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
vg1124078018 4.86E-06 NA mr1246_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
vg1124078018 NA 5.08E-06 mr1407_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
vg1124078018 4.33E-06 3.72E-06 mr1595_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
vg1124078018 NA 2.34E-06 mr1600_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
vg1124078018 5.93E-06 2.64E-06 mr1609_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
vg1124078018 5.07E-06 NA mr1763_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
vg1124078018 3.87E-08 3.87E-08 mr1852_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
vg1124078018 NA 6.77E-06 mr1888_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
vg1124078018 6.86E-07 1.63E-06 mr1909_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