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Detailed information for vg1110664454:

Variant ID: vg1110664454 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 10664454
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CGATCCACTTGGTGAATTTATCGATCGCCACGAATAGAAATTTGTAGCCGCCCTGTCCTCGTGGGAATGGTCCGAGTATATCGAGCCCCCAGCACGAGAA[C/T]
GACCAAGTAAGAGGGATAGTCTGGAGCACTTGCGCTGGCAGTTTTGTGTGTTTGCTGTGAAATTGATAGGCTTCACACCGCTGCACCATGTCGCAGGCGT

Reverse complement sequence

ACGCCTGCGACATGGTGCAGCGGTGTGAAGCCTATCAATTTCACAGCAAACACACAAAACTGCCAGCGCAAGTGCTCCAGACTATCCCTCTTACTTGGTC[G/A]
TTCTCGTGCTGGGGGCTCGATATACTCGGACCATTCCCACGAGGACAGGGCGGCTACAAATTTCTATTCGTGGCGATCGATAAATTCACCAAGTGGATCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 5.30% 0.61% 3.53% NA
All Indica  2759 93.20% 1.20% 0.87% 4.75% NA
All Japonica  1512 97.50% 0.70% 0.00% 1.79% NA
Aus  269 46.80% 50.90% 1.49% 0.74% NA
Indica I  595 87.40% 0.00% 3.53% 9.08% NA
Indica II  465 96.30% 0.20% 0.22% 3.23% NA
Indica III  913 98.40% 1.30% 0.11% 0.22% NA
Indica Intermediate  786 89.80% 2.40% 0.13% 7.63% NA
Temperate Japonica  767 97.90% 0.30% 0.00% 1.83% NA
Tropical Japonica  504 97.20% 0.20% 0.00% 2.58% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 68.80% 0.00% 2.08% NA
Intermediate  90 86.70% 6.70% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1110664454 C -> T LOC_Os11g18790.1 synonymous_variant ; p.Ser767Ser; LOW synonymous_codon Average:56.654; most accessible tissue: Minghui63 flag leaf, score: 72.472 N N N N
vg1110664454 C -> T LOC_Os11g18790.1 synonymous_variant ; p.Ser767Ser; LOW nonsynonymous_codon ; S767P Average:56.654; most accessible tissue: Minghui63 flag leaf, score: 72.472 benign -0.582 TOLERATED 1.00
vg1110664454 C -> T LOC_Os11g18790.1 synonymous_variant ; p.Ser767Ser; LOW nonsynonymous_codon ; S767L Average:56.654; most accessible tissue: Minghui63 flag leaf, score: 72.472 benign -0.036 DELETERIOUS 0.05
vg1110664454 C -> DEL LOC_Os11g18790.1 N frameshift_variant Average:56.654; most accessible tissue: Minghui63 flag leaf, score: 72.472 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1110664454 NA 4.00E-06 mr1073 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
vg1110664454 NA 4.70E-15 mr1113 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
vg1110664454 NA 1.58E-17 mr1114 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
vg1110664454 NA 1.20E-18 mr1117 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
vg1110664454 NA 5.81E-18 mr1119 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
vg1110664454 NA 4.04E-23 mr1247 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
vg1110664454 NA 1.96E-06 mr1510 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
vg1110664454 1.30E-11 2.21E-45 mr1550 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
vg1110664454 NA 3.95E-18 mr1113_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
vg1110664454 NA 1.05E-17 mr1114_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
vg1110664454 NA 3.24E-18 mr1117_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
vg1110664454 NA 2.06E-17 mr1119_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
vg1110664454 NA 1.48E-21 mr1120_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
vg1110664454 NA 9.21E-18 mr1240_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
vg1110664454 2.13E-11 2.03E-48 mr1550_2 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