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Detailed information for vg1121950694:

Variant ID: vg1121950694 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21950694
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GATCAAGCGGAAGATTTCCGATTATCCTCGGCAATGGCATACTCGATTGGCCGAAGCATTCTGGTCTTATAGGATGGCTTGTCATGGATCGATCCAAGTT[C/T]
CTCCTTACAAACTTGTTTATGGACATGAGGCTGTTTTACCATGGGAAGTTAGAATCGGCTCTCGACAAACGGAGTTGCAAAATGATTTGACAGCCGACGA

Reverse complement sequence

TCGTCGGCTGTCAAATCATTTTGCAACTCCGTTTGTCGAGAGCCGATTCTAACTTCCCATGGTAAAACAGCCTCATGTCCATAAACAAGTTTGTAAGGAG[G/A]
AACTTGGATCGATCCATGACAAGCCATCCTATAAGACCAGAATGCTTCGGCCAATCGAGTATGCCATTGCCGAGGATAATCGGAAATCTTCCGCTTGATC

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 90.30% 6.10% 2.09% 1.50% NA
All Indica  2759 91.00% 6.90% 1.45% 0.65% NA
All Japonica  1512 90.80% 6.30% 2.05% 0.79% NA
Aus  269 79.60% 0.00% 6.32% 14.13% NA
Indica I  595 92.80% 7.10% 0.17% 0.00% NA
Indica II  465 99.10% 0.60% 0.00% 0.22% NA
Indica III  913 86.90% 9.10% 3.07% 0.99% NA
Indica Intermediate  786 89.80% 7.80% 1.40% 1.02% NA
Temperate Japonica  767 85.30% 11.90% 2.87% 0.00% NA
Tropical Japonica  504 96.60% 0.40% 1.59% 1.39% NA
Japonica Intermediate  241 96.30% 1.20% 0.41% 2.07% NA
VI/Aromatic  96 89.60% 0.00% 8.33% 2.08% NA
Intermediate  90 91.10% 4.40% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121950694 C -> T LOC_Os11g37170.1 missense_variant ; p.Pro1558Ser; MODERATE nonsynonymous_codon ; P1558S Average:27.14; most accessible tissue: Minghui63 flag leaf, score: 40.473 benign 0.814 DELETERIOUS 0.04
vg1121950694 C -> DEL LOC_Os11g37170.1 N frameshift_variant Average:27.14; most accessible tissue: Minghui63 flag leaf, score: 40.473 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121950694 NA 6.96E-10 mr1210 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
vg1121950694 NA 2.04E-09 mr1305 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
vg1121950694 3.23E-07 3.23E-07 mr1409 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
vg1121950694 NA 7.71E-11 mr1585 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
vg1121950694 NA 8.86E-09 mr1586 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
vg1121950694 NA 2.09E-06 mr1765 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
vg1121950694 2.49E-06 2.49E-06 mr1804 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
vg1121950694 6.79E-06 1.26E-09 mr1305_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
vg1121950694 9.11E-06 1.30E-07 mr1409_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
vg1121950694 NA 9.36E-06 mr1559_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
vg1121950694 NA 1.36E-12 mr1585_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
vg1121950694 NA 3.97E-07 mr1765_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