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Detailed information for vg0809553553:

Variant ID: vg0809553553 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9553553
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGTTGCTTCAGAGGGTTCTAGGCCAGTATTGCTATTCGACTTGTACCGGCTTGCACCGCATGTTGGACATTCATCTAAAGAAGCGTACTCTTTCTTGTA[C/T]
AGTATGCAGTGATTTACGCACATATGAATCTTTTCCACACCAAGTGAAAGGGGGCATATGAGTTTCTTTGCTTGATATGTGTTGGATGGTAGTGAGTTAG

Reverse complement sequence

CTAACTCACTACCATCCAACACATATCAAGCAAAGAAACTCATATGCCCCCTTTCACTTGGTGTGGAAAAGATTCATATGTGCGTAAATCACTGCATACT[G/A]
TACAAGAAAGAGTACGCTTCTTTAGATGAATGTCCAACATGCGGTGCAAGCCGGTACAAGTCGAATAGCAATACTGGCCTAGAACCCTCTGAAGCAACTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 17.00% 5.00% 6.58% 71.46% NA
All Indica  2759 5.00% 7.80% 10.04% 77.13% NA
All Japonica  1512 42.10% 1.10% 1.52% 55.29% NA
Aus  269 2.20% 0.00% 1.12% 96.65% NA
Indica I  595 13.30% 1.00% 1.18% 84.54% NA
Indica II  465 3.00% 15.30% 18.06% 63.66% NA
Indica III  913 0.30% 9.40% 10.30% 79.96% NA
Indica Intermediate  786 5.30% 6.70% 11.70% 76.21% NA
Temperate Japonica  767 73.10% 0.30% 0.00% 26.60% NA
Tropical Japonica  504 2.20% 3.00% 4.56% 90.28% NA
Japonica Intermediate  241 26.60% 0.00% 0.00% 73.44% NA
VI/Aromatic  96 1.00% 0.00% 2.08% 96.88% NA
Intermediate  90 23.30% 3.30% 6.67% 66.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0809553553 C -> T LOC_Os08g15760.1 synonymous_variant ; p.Leu128Leu; LOW synonymous_codon Average:8.695; most accessible tissue: Minghui63 young leaf, score: 13.864 N N N N
vg0809553553 C -> DEL LOC_Os08g15760.1 N frameshift_variant Average:8.695; most accessible tissue: Minghui63 young leaf, score: 13.864 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809553553 NA 2.66E-12 mr1069 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
vg0809553553 4.83E-06 7.70E-06 mr1069 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
vg0809553553 NA 9.69E-06 mr1224 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
vg0809553553 NA 6.45E-06 mr1404 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
vg0809553553 NA 2.85E-07 mr1780 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
vg0809553553 NA 3.51E-06 mr1918 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