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Detailed information for vg0504757155:

Variant ID: vg0504757155 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 4757155
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAGCCTCTTGGGGAAGATCAACACCAATGACATGTACAAGTTGAAGAAGGAGGAGATGGAGGAAGCCTCACCTTCCAAGAAGTGCATTGCTCTCCAAGC[C/T]
GAAGTTGAAGATAAGGACAAGGGCAAGGTGAATGAAGCCAATGAGGACTTGGAGGAAGAGATTGTCCTTCTTGCTAGAAGGTTCAATGATCTCTTGGGAA

Reverse complement sequence

TTCCCAAGAGATCATTGAACCTTCTAGCAAGAAGGACAATCTCTTCCTCCAAGTCCTCATTGGCTTCATTCACCTTGCCCTTGTCCTTATCTTCAACTTC[G/A]
GCTTGGAGAGCAATGCACTTCTTGGAAGGTGAGGCTTCCTCCATCTCCTCCTTCTTCAACTTGTACATGTCATTGGTGTTGATCTTCCCCAAGAGGCTTG

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 56.40% 36.20% 5.14% 2.20% NA
All Indica  2759 83.00% 4.60% 8.70% 3.70% NA
All Japonica  1512 2.10% 97.90% 0.07% 0.00% NA
Aus  269 90.00% 9.30% 0.37% 0.37% NA
Indica I  595 82.90% 3.90% 10.76% 2.52% NA
Indica II  465 81.70% 7.30% 8.17% 2.80% NA
Indica III  913 84.30% 2.20% 8.76% 4.71% NA
Indica Intermediate  786 82.30% 6.40% 7.38% 3.94% NA
Temperate Japonica  767 1.70% 98.20% 0.13% 0.00% NA
Tropical Japonica  504 1.80% 98.20% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 34.40% 63.30% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0504757155 C -> T LOC_Os05g08694.1 synonymous_variant ; p.Ala126Ala; LOW synonymous_codon Average:17.289; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 N N N N
vg0504757155 C -> DEL LOC_Os05g08694.1 N frameshift_variant Average:17.289; most accessible tissue: Zhenshan97 flag leaf, score: 26.688 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0504757155 NA 1.70E-10 mr1322 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
vg0504757155 NA 8.53E-16 mr1324 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
vg0504757155 NA 5.93E-12 mr1325 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
vg0504757155 NA 2.23E-14 mr1326 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
vg0504757155 NA 3.10E-13 mr1335 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
vg0504757155 NA 2.20E-06 mr1527 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
vg0504757155 NA 2.01E-07 mr1604 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
vg0504757155 NA 4.33E-10 mr1322_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
vg0504757155 NA 9.03E-16 mr1324_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
vg0504757155 NA 1.56E-13 mr1325_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
vg0504757155 NA 3.90E-16 mr1326_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
vg0504757155 NA 2.07E-15 mr1333_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
vg0504757155 NA 5.48E-11 mr1379_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
vg0504757155 NA 1.08E-06 mr1559_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
vg0504757155 NA 4.37E-16 mr1686_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
vg0504757155 NA 2.04E-09 mr1690_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
vg0504757155 NA 6.36E-07 mr1819_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