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Detailed information for vg1220338644:

Variant ID: vg1220338644 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20338644
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTGAGTGCACGGTTATGTCATTTGGACTCACCAATGCACCGGCTTTCTTCATGAACTTAATGAACAAAGTGTTTATGGAGTTTCTTGACAAGTTTGTC[A/G]
TGGTATTCATTGACGACATACTTATTTATTCAAAATCAGAAGAGGAACATGAGCAGCATCTCCGTCTTGTACTCGAGAAATTGAAGGAGCACCAGTTATA

Reverse complement sequence

TATAACTGGTGCTCCTTCAATTTCTCGAGTACAAGACGGAGATGCTGCTCATGTTCCTCTTCTGATTTTGAATAAATAAGTATGTCGTCAATGAATACCA[T/C]
GACAAACTTGTCAAGAAACTCCATAAACACTTTGTTCATTAAGTTCATGAAGAAAGCCGGTGCATTGGTGAGTCCAAATGACATAACCGTGCACTCAAAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.70% 0.20% 4.99% 16.17% NA
All Indica  2759 81.70% 0.30% 4.46% 13.56% NA
All Japonica  1512 74.30% 0.10% 3.77% 21.76% NA
Aus  269 68.80% 0.00% 17.84% 13.38% NA
Indica I  595 85.20% 0.30% 1.85% 12.61% NA
Indica II  465 76.10% 0.20% 6.24% 17.42% NA
Indica III  913 83.00% 0.00% 5.04% 11.94% NA
Indica Intermediate  786 80.90% 0.50% 4.71% 13.87% NA
Temperate Japonica  767 97.30% 0.00% 0.13% 2.61% NA
Tropical Japonica  504 37.50% 0.40% 9.72% 52.38% NA
Japonica Intermediate  241 78.40% 0.00% 2.90% 18.67% NA
VI/Aromatic  96 86.50% 0.00% 5.21% 8.33% NA
Intermediate  90 77.80% 0.00% 3.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220338644 A -> DEL LOC_Os12g33690.1 N frameshift_variant Average:11.889; most accessible tissue: Callus, score: 16.536 N N N N
vg1220338644 A -> G LOC_Os12g33690.1 missense_variant ; p.Met672Val; MODERATE nonsynonymous_codon ; M672V Average:11.889; most accessible tissue: Callus, score: 16.536 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220338644 NA 2.22E-16 mr1156 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
vg1220338644 4.95E-13 3.64E-97 mr1334 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
vg1220338644 3.38E-09 1.86E-12 mr1334 Ind_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
vg1220338644 NA 2.48E-16 mr1334 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
vg1220338644 NA 8.63E-07 mr1587 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
vg1220338644 NA 3.63E-20 mr1588 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
vg1220338644 4.81E-13 2.93E-105 mr1334_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
vg1220338644 4.78E-07 8.63E-11 mr1334_2 Ind_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
vg1220338644 NA 1.34E-18 mr1334_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
vg1220338644 NA 1.32E-14 mr1790_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
vg1220338644 NA 2.16E-08 mr1991_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