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Detailed information for vg0805498945:

Variant ID: vg0805498945 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5498945
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCCCCCAGACAGCAAACGGCCACGAAAGAGGTATGGTCTGCAGGGCCTGGGCCGGCTGATGGGTTTGCCTGGCGTGGAACTGGCACGCCCTACACCGCC[G/A]
GACCAGGTCGACCGCATCATTGAGAGCCGTCGGCCAATAGAAACCTTGGCGAAAGGCCTTGCCAACCAAGGTGCGTGAGGCGGAGTGGGCTCCGCACTCG

Reverse complement sequence

CGAGTGCGGAGCCCACTCCGCCTCACGCACCTTGGTTGGCAAGGCCTTTCGCCAAGGTTTCTATTGGCCGACGGCTCTCAATGATGCGGTCGACCTGGTC[C/T]
GGCGGTGTAGGGCGTGCCAGTTCCACGCCAGGCAAACCCATCAGCCGGCCCAGGCCCTGCAGACCATACCTCTTTCGTGGCCGTTTGCTGTCTGGGGGCT

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 63.90% 1.20% 8.44% 26.47% NA
All Indica  2759 52.00% 2.10% 11.49% 34.47% NA
All Japonica  1512 90.50% 0.00% 2.45% 7.08% NA
Aus  269 44.60% 0.00% 11.15% 44.24% NA
Indica I  595 26.10% 4.50% 7.06% 62.35% NA
Indica II  465 52.30% 2.40% 13.12% 32.26% NA
Indica III  913 72.10% 0.10% 11.83% 15.99% NA
Indica Intermediate  786 48.10% 2.30% 13.49% 36.13% NA
Temperate Japonica  767 96.50% 0.00% 0.39% 3.13% NA
Tropical Japonica  504 84.70% 0.00% 5.75% 9.52% NA
Japonica Intermediate  241 83.40% 0.00% 2.07% 14.52% NA
VI/Aromatic  96 44.80% 0.00% 8.33% 46.88% NA
Intermediate  90 60.00% 0.00% 7.78% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805498945 G -> A LOC_Os08g09500.1 missense_variant ; p.Arg1529Trp; MODERATE nonsynonymous_codon ; R1529W Average:12.106; most accessible tissue: Minghui63 panicle, score: 25.313 benign 1.332 DELETERIOUS 0.02
vg0805498945 G -> DEL LOC_Os08g09500.1 N frameshift_variant Average:12.106; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805498945 NA 1.97E-06 mr1349 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
vg0805498945 6.14E-06 6.14E-06 mr1349 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