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Detailed information for vg1216555105:

Variant ID: vg1216555105 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16555105
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCCCTCCTCCCCCCCTTGGGCTAGATCTGGGAGAGAGGGGAGGGGAGCCGCGCCGACCCTGTCGCCTCGCCGTTGCCGCCGTTGACCCCGCCGCCTCC[A/G]
CGCCTCGCCATTGCCAACCCCGCCGCCTCCCATCGCCATGCTGAGGGAGCTAAGGGAGAGGAGTGGTGAGGCCTGAGGGAGAGGAGAGCTGTGAGCCTGT

Reverse complement sequence

ACAGGCTCACAGCTCTCCTCTCCCTCAGGCCTCACCACTCCTCTCCCTTAGCTCCCTCAGCATGGCGATGGGAGGCGGCGGGGTTGGCAATGGCGAGGCG[T/C]
GGAGGCGGCGGGGTCAACGGCGGCAACGGCGAGGCGACAGGGTCGGCGCGGCTCCCCTCCCCTCTCTCCCAGATCTAGCCCAAGGGGGGGAGGAGGGAGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.10% 19.10% 3.20% 4.57% NA
All Indica  2759 86.90% 5.10% 5.18% 2.75% NA
All Japonica  1512 51.10% 48.70% 0.20% 0.07% NA
Aus  269 48.30% 0.70% 0.37% 50.56% NA
Indica I  595 90.10% 2.00% 6.89% 1.01% NA
Indica II  465 95.30% 3.70% 0.43% 0.65% NA
Indica III  913 83.10% 6.70% 5.91% 4.27% NA
Indica Intermediate  786 84.00% 6.60% 5.85% 3.56% NA
Temperate Japonica  767 19.60% 80.10% 0.26% 0.13% NA
Tropical Japonica  504 95.80% 4.00% 0.20% 0.00% NA
Japonica Intermediate  241 57.70% 42.30% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 0.00% 2.08% NA
Intermediate  90 70.00% 24.40% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216555105 A -> DEL N N silent_mutation Average:73.512; most accessible tissue: Minghui63 panicle, score: 87.605 N N N N
vg1216555105 A -> G LOC_Os12g28050-LOC_Os12g28065 intergenic_region ; MODIFIER silent_mutation Average:73.512; most accessible tissue: Minghui63 panicle, score: 87.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216555105 NA 6.25E-06 mr1271 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
vg1216555105 NA 1.73E-15 mr1401 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
vg1216555105 NA 3.82E-07 mr1401 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
vg1216555105 NA 6.18E-06 mr1942 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
vg1216555105 NA 7.59E-07 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
vg1216555105 1.99E-08 NA mr1071_2 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
vg1216555105 4.77E-06 NA mr1080_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
vg1216555105 NA 1.27E-09 mr1089_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
vg1216555105 NA 7.43E-07 mr1129_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
vg1216555105 1.71E-06 1.71E-06 mr1162_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
vg1216555105 NA 6.77E-13 mr1182_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
vg1216555105 8.22E-08 NA mr1203_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
vg1216555105 NA 2.64E-07 mr1257_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
vg1216555105 NA 4.61E-10 mr1282_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
vg1216555105 6.03E-10 NA mr1613_2 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
vg1216555105 NA 1.33E-07 mr1629_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
vg1216555105 NA 1.32E-06 mr1653_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
vg1216555105 1.17E-06 1.17E-06 mr1754_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
vg1216555105 NA 4.88E-09 mr1805_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
vg1216555105 NA 2.62E-07 mr1821_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