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Detailed information for vg1124618323:

Variant ID: vg1124618323 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24618323
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGCAAATTTAAACGATGTGTTTATGCAAGGAAATAAAAAGTTGTGTGGAGGTTCTCCAATGCTACATTTACCACTTTGCAAGGATTTGTCATCCAAA[A/C]
GGAAAAGGACACCTTATATTCTTGGTGTAGTCATTCCAATCACTACCATTGTTATAGTCACCTTGGTATGTGTTGCCATCATTCTTATGAAGAAGAGAAC

Reverse complement sequence

GTTCTCTTCTTCATAAGAATGATGGCAACACATACCAAGGTGACTATAACAATGGTAGTGATTGGAATGACTACACCAAGAATATAAGGTGTCCTTTTCC[T/G]
TTTGGATGACAAATCCTTGCAAAGTGGTAAATGTAGCATTGGAGAACCTCCACACAACTTTTTATTTCCTTGCATAAACACATCGTTTAAATTTGCAAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.90% 22.90% 1.08% 38.04% NA
All Indica  2759 47.60% 1.30% 1.38% 49.76% NA
All Japonica  1512 18.40% 64.60% 0.60% 16.47% NA
Aus  269 59.50% 13.80% 0.74% 26.02% NA
Indica I  595 62.00% 0.50% 0.67% 36.81% NA
Indica II  465 14.80% 2.20% 2.37% 80.65% NA
Indica III  913 55.00% 0.80% 1.20% 43.04% NA
Indica Intermediate  786 47.30% 2.00% 1.53% 49.11% NA
Temperate Japonica  767 31.40% 53.10% 0.78% 14.73% NA
Tropical Japonica  504 2.00% 78.00% 0.20% 19.84% NA
Japonica Intermediate  241 11.20% 73.00% 0.83% 14.94% NA
VI/Aromatic  96 22.90% 8.30% 1.04% 67.71% NA
Intermediate  90 23.30% 30.00% 1.11% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124618323 A -> DEL LOC_Os11g41100.1 N frameshift_variant Average:28.65; most accessible tissue: Zhenshan97 root, score: 66.289 N N N N
vg1124618323 A -> C LOC_Os11g41100.1 synonymous_variant ; p.Arg737Arg; LOW synonymous_codon Average:28.65; most accessible tissue: Zhenshan97 root, score: 66.289 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124618323 NA 1.26E-26 mr1238 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
vg1124618323 7.62E-08 1.08E-19 mr1900 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
vg1124618323 NA 3.08E-06 mr1786_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
vg1124618323 8.38E-07 5.60E-23 mr1900_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
vg1124618323 NA 3.18E-18 mr1945_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