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Detailed information for vg1220441290:

Variant ID: vg1220441290 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20441290
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGGATTCCTGCCAAAGATTGAGGTAACTCCAACTGATAAGCAACCTCTCCTCTTCTACTGACAATCTTATAAGGTCCCACAAAACGCGGTGCCAATTTT[T/C]
CCTTGGTATGAAAACGATGAACTCCTCGAAAAGGCGTGACACGAAGATACACATAGTCTCCTTCTTCAAAACTCAAATCTCTACGGCGATTGTCGGCATA

Reverse complement sequence

TATGCCGACAATCGCCGTAGAGATTTGAGTTTTGAAGAAGGAGACTATGTGTATCTTCGTGTCACGCCTTTTCGAGGAGTTCATCGTTTTCATACCAAGG[A/G]
AAAATTGGCACCGCGTTTTGTGGGACCTTATAAGATTGTCAGTAGAAGAGGAGAGGTTGCTTATCAGTTGGAGTTACCTCAATCTTTGGCAGGAATCCAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 20.40% 2.50% 21.88% 55.23% NA
All Indica  2759 2.60% 0.00% 29.32% 68.07% NA
All Japonica  1512 55.40% 6.50% 6.75% 31.35% NA
Aus  269 7.40% 4.80% 26.39% 61.34% NA
Indica I  595 3.40% 0.00% 12.61% 84.03% NA
Indica II  465 4.70% 0.00% 27.74% 67.53% NA
Indica III  913 1.20% 0.00% 41.07% 57.72% NA
Indica Intermediate  786 2.40% 0.00% 29.26% 68.32% NA
Temperate Japonica  767 84.70% 6.50% 3.13% 5.61% NA
Tropical Japonica  504 11.90% 2.60% 10.52% 75.00% NA
Japonica Intermediate  241 53.10% 14.50% 10.37% 21.99% NA
VI/Aromatic  96 10.40% 3.10% 33.33% 53.12% NA
Intermediate  90 26.70% 4.40% 22.22% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220441290 T -> C LOC_Os12g33910.1 missense_variant ; p.Glu1285Gly; MODERATE nonsynonymous_codon ; E1285G Average:6.979; most accessible tissue: Minghui63 flower, score: 11.139 unknown unknown TOLERATED 1.00
vg1220441290 T -> DEL LOC_Os12g33910.1 N frameshift_variant Average:6.979; most accessible tissue: Minghui63 flower, score: 11.139 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220441290 NA 6.95E-10 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1220441290 1.44E-06 1.17E-08 mr1057 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
vg1220441290 NA 6.01E-08 mr1057 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
vg1220441290 NA 8.38E-08 mr1201 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
vg1220441290 NA 1.16E-06 mr1219 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
vg1220441290 NA 7.57E-07 mr1274 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
vg1220441290 9.17E-06 NA mr1565 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
vg1220441290 5.52E-06 NA mr1887 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
vg1220441290 NA 2.32E-08 mr1057_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
vg1220441290 NA 8.85E-10 mr1057_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
vg1220441290 NA 6.89E-08 mr1624_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