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Detailed information for vg0805024489:

Variant ID: vg0805024489 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 5024489
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCAATACATTCAAAATAGTTTACATCGTGTACACAACAATTACGGCAATACATCGGCGGTGACGGTTGACCACACGTACTTTCTCCTCACTATTGTTCC[T/C]
TCCTTGTGATCGCTACGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGGTCAATCGTCACCGTGAAAGGGGGTTGCCCATCAAACTGATCGTAATC

Reverse complement sequence

GATTACGATCAGTTTGATGGGCAACCCCCTTTCACGGTGACGATTGACCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACGTAGCGATCACAAGGA[A/G]
GGAACAATAGTGAGGAGAAAGTACGTGTGGTCAACCGTCACCGCCGATGTATTGCCGTAATTGTTGTGTACACGATGTAAACTATTTTGAATGTATTGAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.60% 0.30% 12.21% 16.93% NA
All Indica  2759 66.90% 0.00% 13.88% 19.17% NA
All Japonica  1512 75.60% 0.80% 8.20% 15.41% NA
Aus  269 80.70% 0.40% 15.24% 3.72% NA
Indica I  595 95.10% 0.00% 0.84% 4.03% NA
Indica II  465 54.00% 0.00% 12.04% 33.98% NA
Indica III  913 52.00% 0.00% 23.88% 24.10% NA
Indica Intermediate  786 70.60% 0.00% 13.23% 16.16% NA
Temperate Japonica  767 91.00% 0.10% 2.09% 6.78% NA
Tropical Japonica  504 50.00% 2.00% 17.66% 30.36% NA
Japonica Intermediate  241 80.10% 0.40% 7.88% 11.62% NA
VI/Aromatic  96 68.80% 0.00% 18.75% 12.50% NA
Intermediate  90 70.00% 0.00% 12.22% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0805024489 T -> C LOC_Os08g08680.1 missense_variant ; p.Lys579Arg; MODERATE nonsynonymous_codon ; K579R Average:16.58; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 unknown unknown DELETERIOUS 0.02
vg0805024489 T -> DEL LOC_Os08g08680.1 N frameshift_variant Average:16.58; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0805024489 NA 1.34E-07 mr1338 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
vg0805024489 NA 4.06E-14 mr1449 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
vg0805024489 NA 2.82E-09 mr1449 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
vg0805024489 NA 7.22E-07 mr1518 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
vg0805024489 NA 7.17E-09 mr1676 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
vg0805024489 1.48E-08 NA mr1113_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
vg0805024489 3.66E-06 NA mr1117_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
vg0805024489 3.80E-06 NA mr1496_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
vg0805024489 3.13E-06 NA mr1961_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