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Detailed information for vg1118715674:

Variant ID: vg1118715674 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18715674
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGCAGGTCTCCGGAACCTCTGCCTTCGACGTCCTGCACCGGGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTCGTGCGACTGCTCCCTGTTTGTT[C/T]
GCGACGGCTCGCCTTCCTCTTCGCTCGCGTGTTTCGTGCCTTCGTAGACACCTGCGAAAAGTTTCAACCAATCAGCCGGTCTTTCCGTCATCTCGGTACG

Reverse complement sequence

CGTACCGAGATGACGGAAAGACCGGCTGATTGGTTGAAACTTTTCGCAGGTGTCTACGAAGGCACGAAACACGCGAGCGAAGAGGAAGGCGAGCCGTCGC[G/A]
AACAAACAGGGAGCAGTCGCACGAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCCCGGTGCAGGACGTCGAAGGCAGAGGTTCCGGAGACCTGCTCT

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 72.10% 0.70% 17.86% 9.35% NA
All Indica  2759 58.80% 0.90% 26.31% 13.95% NA
All Japonica  1512 96.00% 0.00% 2.18% 1.79% NA
Aus  269 74.30% 2.20% 20.07% 3.35% NA
Indica I  595 39.00% 0.00% 43.53% 17.48% NA
Indica II  465 51.40% 0.90% 29.03% 18.71% NA
Indica III  913 74.00% 1.40% 15.99% 8.54% NA
Indica Intermediate  786 60.60% 1.00% 23.66% 14.76% NA
Temperate Japonica  767 96.00% 0.00% 2.61% 1.43% NA
Tropical Japonica  504 96.00% 0.00% 1.98% 1.98% NA
Japonica Intermediate  241 96.30% 0.00% 1.24% 2.49% NA
VI/Aromatic  96 77.10% 0.00% 15.62% 7.29% NA
Intermediate  90 66.70% 0.00% 17.78% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1118715674 C -> T LOC_Os11g31850.1 downstream_gene_variant ; 2786.0bp to feature; MODIFIER silent_mutation Average:31.577; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg1118715674 C -> T LOC_Os11g31840.1 intron_variant ; MODIFIER silent_mutation Average:31.577; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N
vg1118715674 C -> DEL N N silent_mutation Average:31.577; most accessible tissue: Zhenshan97 panicle, score: 54.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118715674 NA 2.66E-06 mr1209 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
vg1118715674 NA 2.68E-06 mr1365 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
vg1118715674 3.75E-06 3.76E-06 mr1385 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
vg1118715674 1.55E-06 1.55E-06 mr1643 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
vg1118715674 1.35E-07 NA mr1248_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
vg1118715674 NA 8.81E-07 mr1252_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
vg1118715674 NA 1.18E-06 mr1263_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
vg1118715674 NA 2.77E-06 mr1740_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