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Detailed information for vg1212722703:

Variant ID: vg1212722703 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 12722703
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, T: 0.08, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCTACTGTTGTGAGACATTAACCGTGCCAACCACAAGCCAGCGTAGGCAACGGCTTTACCTTTTGTATAGCATGATTCATTACGGGGTGCCAGACTGA[T/G]
AAGCGGTGAGAAGTCCGTGGGGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGT

Reverse complement sequence

ACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCCCCACGGACTTCTCACCGCTT[A/C]
TCAGTCTGGCACCCCGTAATGAATCATGCTATACAAAAGGTAAAGCCGTTGCCTACGCTGGCTTGTGGTTGGCACGGTTAATGTCTCACAACAGTAGCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.90% 15.70% 0.06% 0.36% NA
All Indica  2759 96.80% 3.10% 0.00% 0.11% NA
All Japonica  1512 56.90% 42.10% 0.20% 0.79% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.20% 2.60% 0.00% 0.22% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 4.70% 0.00% 0.25% NA
Temperate Japonica  767 23.10% 75.20% 0.26% 1.43% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.00% 0.41% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 20.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1212722703 T -> DEL LOC_Os12g22540.1 N frameshift_variant Average:52.856; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg1212722703 T -> G LOC_Os12g22540.1 missense_variant ; p.Ile21Arg; MODERATE nonsynonymous_codon ; I21R Average:52.856; most accessible tissue: Minghui63 young leaf, score: 75.006 unknown unknown TOLERATED 0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1212722703 NA 1.88E-60 mr1023 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
vg1212722703 NA 4.75E-15 mr1023 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
vg1212722703 NA 6.35E-10 mr1178 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
vg1212722703 NA 3.06E-69 mr1489 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
vg1212722703 NA 3.72E-14 mr1489 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
vg1212722703 NA 3.63E-14 mr1491 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
vg1212722703 NA 5.86E-08 mr1606 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
vg1212722703 NA 2.32E-06 mr1606 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
vg1212722703 NA 6.39E-06 mr1657 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
vg1212722703 NA 3.65E-16 mr1013_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
vg1212722703 NA 3.41E-72 mr1023_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
vg1212722703 NA 5.07E-15 mr1031_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
vg1212722703 NA 7.63E-54 mr1079_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
vg1212722703 NA 2.18E-08 mr1338_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
vg1212722703 NA 8.89E-09 mr1471_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
vg1212722703 NA 1.29E-78 mr1489_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
vg1212722703 NA 9.68E-08 mr1606_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
vg1212722703 NA 1.51E-12 mr1722_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
vg1212722703 NA 5.05E-13 mr1879_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