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Detailed information for vg1105930906:

Variant ID: vg1105930906 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5930906
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CCGATATTGTTTCCGTTACCATCTTACCGTTATCGATTCTGTTTCAGAAAAATAATATGGTTGTGGTAATGGTTTAGGGTTTTTCCTGATCGTTTCCGAC[T/C]
GCTTTCACCCCTATCACTGCATCACCTTGATCACCACCACATATCTACACCATGCTTGTTGTCTTGTGGCCATGAACCGCTCCGTCGAATCACAGCCTTG

Reverse complement sequence

CAAGGCTGTGATTCGACGGAGCGGTTCATGGCCACAAGACAACAAGCATGGTGTAGATATGTGGTGGTGATCAAGGTGATGCAGTGATAGGGGTGAAAGC[A/G]
GTCGGAAACGATCAGGAAAAACCCTAAACCATTACCACAACCATATTATTTTTCTGAAACAGAATCGATAACGGTAAGATGGTAACGGAAACAATATCGG

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 26.40% 11.50% 3.41% 58.74% NA
All Indica  2759 16.70% 2.20% 1.70% 79.38% NA
All Japonica  1512 45.30% 28.70% 6.75% 19.25% NA
Aus  269 5.90% 0.00% 1.86% 92.19% NA
Indica I  595 0.80% 2.40% 4.03% 92.77% NA
Indica II  465 9.20% 0.60% 1.51% 88.60% NA
Indica III  913 26.90% 2.50% 0.11% 70.43% NA
Indica Intermediate  786 21.40% 2.50% 1.91% 74.17% NA
Temperate Japonica  767 16.30% 42.40% 10.17% 31.16% NA
Tropical Japonica  504 88.10% 6.00% 1.98% 3.97% NA
Japonica Intermediate  241 48.10% 32.80% 5.81% 13.28% NA
VI/Aromatic  96 46.90% 40.60% 2.08% 10.42% NA
Intermediate  90 42.20% 11.10% 5.56% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105930906 T -> DEL N N silent_mutation Average:9.337; most accessible tissue: Callus, score: 51.373 N N N N
vg1105930906 T -> C LOC_Os11g10780-LOC_Os11g10790 intergenic_region ; MODIFIER silent_mutation Average:9.337; most accessible tissue: Callus, score: 51.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105930906 3.96E-06 NA mr1071 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
vg1105930906 1.88E-06 NA mr1137 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
vg1105930906 2.68E-06 NA mr1140 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
vg1105930906 2.38E-07 NA mr1203 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
vg1105930906 NA 8.44E-06 mr1354 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
vg1105930906 NA 1.54E-07 mr1364 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
vg1105930906 1.99E-08 NA mr1618 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
vg1105930906 NA 3.68E-06 mr1618 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
vg1105930906 NA 4.05E-07 mr1884 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
vg1105930906 7.28E-07 NA mr1768_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