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Detailed information for vg0804838042:

Variant ID: vg0804838042 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4838042
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTGATTGACGATCTATGGGAAACGTTCGACAACCTCCGATGATATCGCCTTATGCTCAATCCAGAGAAGTGCACGTTCAGAGTACCGTCGGGCAAGCT[G/T]
CTCGGTTTCCTCGTATCTGGCAGAGGAATAGAAGCAAATCCCGAGAAGATCAAAGCAATCGAGAACATGAAGTCGCCCAAAAGACTCAAGGAAGTACAAA

Reverse complement sequence

TTTGTACTTCCTTGAGTCTTTTGGGCGACTTCATGTTCTCGATTGCTTTGATCTTCTCGGGATTTGCTTCTATTCCTCTGCCAGATACGAGGAAACCGAG[C/A]
AGCTTGCCCGACGGTACTCTGAACGTGCACTTCTCTGGATTGAGCATAAGGCGATATCATCGGAGGTTGTCGAACGTTTCCCATAGATCGTCAATCAATG

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 53.00% 2.90% 13.46% 30.68% NA
All Indica  2759 33.30% 4.70% 19.75% 42.23% NA
All Japonica  1512 88.60% 0.00% 0.93% 10.52% NA
Aus  269 66.90% 0.00% 18.96% 14.13% NA
Indica I  595 21.50% 0.00% 17.98% 60.50% NA
Indica II  465 29.20% 24.10% 18.71% 27.96% NA
Indica III  913 41.80% 0.10% 20.37% 37.68% NA
Indica Intermediate  786 34.60% 2.30% 20.99% 42.11% NA
Temperate Japonica  767 90.60% 0.00% 0.78% 8.60% NA
Tropical Japonica  504 88.30% 0.00% 1.19% 10.52% NA
Japonica Intermediate  241 82.60% 0.00% 0.83% 16.60% NA
VI/Aromatic  96 20.80% 2.10% 13.54% 63.54% NA
Intermediate  90 53.30% 2.20% 14.44% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0804838042 G -> T LOC_Os08g08390.1 missense_variant ; p.Ala788Ser; MODERATE nonsynonymous_codon ; A788S Average:18.058; most accessible tissue: Minghui63 root, score: 40.262 unknown unknown TOLERATED 0.83
vg0804838042 G -> DEL LOC_Os08g08390.1 N frameshift_variant Average:18.058; most accessible tissue: Minghui63 root, score: 40.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804838042 NA 1.15E-07 mr1089 Ind_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
vg0804838042 NA 2.18E-08 mr1093 Ind_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
vg0804838042 NA 6.25E-06 mr1129 Ind_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
vg0804838042 NA 7.24E-06 mr1235 Ind_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
vg0804838042 NA 2.69E-07 mr1243 Ind_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
vg0804838042 NA 6.29E-06 mr1251 Ind_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
vg0804838042 NA 2.77E-07 mr1257 Ind_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
vg0804838042 NA 1.39E-07 mr1410 Ind_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
vg0804838042 3.54E-06 1.45E-09 mr1423 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
vg0804838042 NA 1.40E-08 mr1435 Ind_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
vg0804838042 NA 8.02E-09 mr1599 Ind_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