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Detailed information for vg1221827817:

Variant ID: vg1221827817 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21827817
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTCAGGAGAAAACAAGTGTGCAGGTGGAGCACTTGATCAGTTCAGGGCATGCACCAGAAAAAGAAGATGTTGCTATTAACCAAGATGCACCTGTTATT[C/G]
AAGATTCAGATTCTTCTATTGTTCATCAGTCTCCCAAACGTTCTATTGCAAAAGATAAGCCCAAAAGAAATATTAAACCACCTCGAAGATATATTGAAGA

Reverse complement sequence

TCTTCAATATATCTTCGAGGTGGTTTAATATTTCTTTTGGGCTTATCTTTTGCAATAGAACGTTTGGGAGACTGATGAACAATAGAAGAATCTGAATCTT[G/C]
AATAACAGGTGCATCTTGGTTAATAGCAACATCTTCTTTTTCTGGTGCATGCCCTGAACTGATCAAGTGCTCCACCTGCACACTTGTTTTCTCCTGACTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.30% 11.90% 26.81% 32.92% NA
All Indica  2759 12.60% 1.30% 36.57% 49.51% NA
All Japonica  1512 56.70% 33.70% 5.62% 3.97% NA
Aus  269 13.80% 0.00% 55.02% 31.23% NA
Indica I  595 14.30% 0.50% 22.69% 62.52% NA
Indica II  465 27.70% 2.20% 38.06% 32.04% NA
Indica III  913 5.60% 1.40% 44.36% 48.63% NA
Indica Intermediate  786 10.40% 1.40% 37.15% 51.02% NA
Temperate Japonica  767 34.80% 55.80% 6.78% 2.61% NA
Tropical Japonica  504 80.40% 9.50% 3.57% 6.55% NA
Japonica Intermediate  241 76.80% 14.10% 6.22% 2.90% NA
VI/Aromatic  96 60.40% 0.00% 6.25% 33.33% NA
Intermediate  90 44.40% 18.90% 21.11% 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
vg1221827817 C -> DEL LOC_Os12g35810.1 N frameshift_variant Average:6.835; most accessible tissue: Minghui63 flower, score: 9.27 N N N N
vg1221827817 C -> G LOC_Os12g35810.1 missense_variant ; p.Gln505Glu; MODERATE nonsynonymous_codon ; Q505E Average:6.835; most accessible tissue: Minghui63 flower, score: 9.27 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221827817 NA 1.30E-07 mr1002 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
vg1221827817 NA 8.07E-08 mr1163 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
vg1221827817 2.94E-06 NA mr1486 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
vg1221827817 NA 5.27E-09 mr1486 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
vg1221827817 NA 3.23E-10 mr1010_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
vg1221827817 NA 1.20E-09 mr1011_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
vg1221827817 NA 3.73E-06 mr1011_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
vg1221827817 NA 5.89E-06 mr1768_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