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Detailed information for vg1127529196:

Variant ID: vg1127529196 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27529196
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAAGTACTTATCTTCTGTCAATGTCTTGAGCGAGTGAAACACTGGTGGAGAAACCATCTTTTGTCGATCGGCCGAATTCCACAATAGTCCCGGTTGCAA[C/T]
AAAAACCGGGACTAAAGATGATCTTTAGTCCCGGTTAAAAAGGGTAACGGGCATATTTGATCTTTAGTCCTGGTTGGTAACACCAACCTCTTTAGTCCCG

Reverse complement sequence

CGGGACTAAAGAGGTTGGTGTTACCAACCAGGACTAAAGATCAAATATGCCCGTTACCCTTTTTAACCGGGACTAAAGATCATCTTTAGTCCCGGTTTTT[G/A]
TTGCAACCGGGACTATTGTGGAATTCGGCCGATCGACAAAAGATGGTTTCTCCACCAGTGTTTCACTCGCTCAAGACATTGACAGAAGATAAGTACTTGC

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 67.80% 0.30% 5.76% 26.22% NA
All Indica  2759 74.00% 0.30% 5.87% 19.90% NA
All Japonica  1512 53.60% 0.00% 5.69% 40.74% NA
Aus  269 75.50% 1.50% 5.95% 17.10% NA
Indica I  595 64.70% 0.30% 4.71% 30.25% NA
Indica II  465 61.90% 0.20% 7.74% 30.11% NA
Indica III  913 85.90% 0.30% 4.38% 9.42% NA
Indica Intermediate  786 74.30% 0.10% 7.38% 18.19% NA
Temperate Japonica  767 46.50% 0.00% 2.09% 51.37% NA
Tropical Japonica  504 64.70% 0.00% 10.52% 24.80% NA
Japonica Intermediate  241 52.70% 0.00% 7.05% 40.25% NA
VI/Aromatic  96 88.50% 2.10% 4.17% 5.21% NA
Intermediate  90 70.00% 0.00% 4.44% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127529196 C -> T LOC_Os11g45470.1 upstream_gene_variant ; 794.0bp to feature; MODIFIER silent_mutation Average:12.574; most accessible tissue: Callus, score: 33.028 N N N N
vg1127529196 C -> T LOC_Os11g45480.1 upstream_gene_variant ; 1837.0bp to feature; MODIFIER silent_mutation Average:12.574; most accessible tissue: Callus, score: 33.028 N N N N
vg1127529196 C -> T LOC_Os11g45460-LOC_Os11g45470 intergenic_region ; MODIFIER silent_mutation Average:12.574; most accessible tissue: Callus, score: 33.028 N N N N
vg1127529196 C -> DEL N N silent_mutation Average:12.574; most accessible tissue: Callus, score: 33.028 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127529196 NA 8.99E-06 mr1069 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
vg1127529196 NA 1.33E-06 mr1101 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
vg1127529196 NA 8.57E-06 mr1858 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
vg1127529196 NA 8.56E-06 mr1859 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
vg1127529196 7.70E-06 5.38E-06 mr1072_2 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
vg1127529196 NA 3.98E-06 mr1075_2 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
vg1127529196 NA 2.54E-07 mr1098_2 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
vg1127529196 7.04E-06 7.08E-07 mr1124_2 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
vg1127529196 2.12E-07 2.23E-10 mr1150_2 Jap_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
vg1127529196 8.59E-07 5.13E-07 mr1200_2 Jap_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
vg1127529196 NA 8.47E-06 mr1240_2 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
vg1127529196 NA 9.45E-06 mr1441_2 Jap_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
vg1127529196 2.18E-06 7.96E-08 mr1861_2 Jap_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