Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0806548377:

Variant ID: vg0806548377 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6548377
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAATTCTTTTTGATCTAGATTCTCGCGGCCCACTGCTCGACCGAGCGAACCATGTGGGCTCATATTGACGGCTTCAAGAACCATCTTCGAGCCAAGGAC[A/G]
ATGAACTGGGTCGCAAGAGCTTGGAGATGGAGGGCCTCGCCAACACCCTCAAAGAGGCGAAGGCTGAGAACAAGTGGCTCCAAGCTGAGCTGGAGAAGGG

Reverse complement sequence

CCCTTCTCCAGCTCAGCTTGGAGCCACTTGTTCTCAGCCTTCGCCTCTTTGAGGGTGTTGGCGAGGCCCTCCATCTCCAAGCTCTTGCGACCCAGTTCAT[T/C]
GTCCTTGGCTCGAAGATGGTTCTTGAAGCCGTCAATATGAGCCCACATGGTTCGCTCGGTCGAGCAGTGGGCCGCGAGAATCTAGATCAAAAAGAATTGA

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 32.70% 13.30% 7.22% 46.72% NA
All Indica  2759 14.00% 9.80% 6.20% 70.03% NA
All Japonica  1512 73.70% 23.30% 0.53% 2.38% NA
Aus  269 1.90% 0.70% 48.33% 49.07% NA
Indica I  595 30.80% 6.10% 2.86% 60.34% NA
Indica II  465 9.50% 2.80% 4.52% 83.23% NA
Indica III  913 5.00% 13.60% 7.45% 73.93% NA
Indica Intermediate  786 14.20% 12.50% 8.27% 65.01% NA
Temperate Japonica  767 55.00% 42.20% 0.78% 1.96% NA
Tropical Japonica  504 96.20% 0.80% 0.40% 2.58% NA
Japonica Intermediate  241 86.30% 10.40% 0.00% 3.32% NA
VI/Aromatic  96 3.10% 1.00% 27.08% 68.75% NA
Intermediate  90 43.30% 3.30% 6.67% 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
vg0806548377 A -> G LOC_Os08g11130.1 missense_variant ; p.Asn532Asp; MODERATE nonsynonymous_codon Average:10.551; most accessible tissue: Callus, score: 28.358 possibly damaging -1.653 TOLERATED 1.00
vg0806548377 A -> DEL LOC_Os08g11130.1 N frameshift_variant Average:10.551; most accessible tissue: Callus, score: 28.358 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806548377 NA 4.40E-17 mr1035 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
vg0806548377 NA 8.61E-07 mr1035 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
vg0806548377 NA 1.53E-13 mr1149 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
vg0806548377 NA 3.21E-08 mr1162 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
vg0806548377 3.33E-06 8.17E-07 mr1415 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
vg0806548377 NA 1.31E-08 mr1510 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
vg0806548377 3.33E-06 8.17E-07 mr1567 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
vg0806548377 NA 4.99E-13 mr1626 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
vg0806548377 NA 4.94E-10 mr1630 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
vg0806548377 NA 5.50E-10 mr1648 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
vg0806548377 NA 2.11E-17 mr1062_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
vg0806548377 NA 7.35E-07 mr1062_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
vg0806548377 NA 6.52E-06 mr1080_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