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Detailed information for vg0613452440:

Variant ID: vg0613452440 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13452440
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GCGAGCGGGGGATGCCCTTTTTCAAGCTGTTGAAGAAAACAGACAACTTCCAATGGGGACCCGAAGCCCAAAAAGCCTTCGAAGACTTCAAAAAACTCCT[T/C]
ACTACTCCACCAGTCTTAGCTTCGCCACATCCGCAAGAGCCGTTGTTGTTATATGTATCGGCAACTTCCCAGGTTATAAGCACAGTCCTGGTCGTCGAGC

Reverse complement sequence

GCTCGACGACCAGGACTGTGCTTATAACCTGGGAAGTTGCCGATACATATAACAACAACGGCTCTTGCGGATGTGGCGAAGCTAAGACTGGTGGAGTAGT[A/G]
AGGAGTTTTTTGAAGTCTTCGAAGGCTTTTTGGGCTTCGGGTCCCCATTGGAAGTTGTCTGTTTTCTTCAACAGCTTGAAAAAGGGCATCCCCCGCTCGC

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 63.90% 33.80% 0.30% 1.99% NA
All Indica  2759 97.10% 2.70% 0.07% 0.11% NA
All Japonica  1512 3.00% 93.50% 0.46% 3.04% NA
Aus  269 55.80% 28.30% 0.74% 15.24% NA
Indica I  595 97.10% 2.70% 0.17% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 95.20% 4.50% 0.00% 0.38% NA
Temperate Japonica  767 3.70% 94.40% 0.00% 1.96% NA
Tropical Japonica  504 2.20% 92.50% 0.99% 4.37% NA
Japonica Intermediate  241 2.50% 92.90% 0.83% 3.73% NA
VI/Aromatic  96 96.90% 2.10% 0.00% 1.04% NA
Intermediate  90 56.70% 36.70% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0613452440 T -> C LOC_Os06g23070.1 synonymous_variant ; p.Leu835Leu; LOW synonymous_codon Average:48.957; most accessible tissue: Minghui63 flag leaf, score: 74.563 N N N N
vg0613452440 T -> DEL LOC_Os06g23070.1 N frameshift_variant Average:48.957; most accessible tissue: Minghui63 flag leaf, score: 74.563 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613452440 NA 1.45E-21 mr1020 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
vg0613452440 2.64E-25 4.18E-93 mr1033 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
vg0613452440 4.56E-14 3.39E-20 mr1033 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
vg0613452440 4.25E-18 1.97E-51 mr1176 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
vg0613452440 2.93E-11 1.36E-14 mr1176 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
vg0613452440 NA 1.43E-20 mr1477 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
vg0613452440 4.99E-08 4.25E-72 mr1536 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
vg0613452440 1.60E-07 1.60E-07 mr1536 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
vg0613452440 NA 3.92E-21 mr1971 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
vg0613452440 1.85E-33 3.00E-129 mr1033_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
vg0613452440 9.83E-17 5.64E-26 mr1033_2 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
vg0613452440 NA 4.88E-20 mr1276_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
vg0613452440 NA 9.48E-30 mr1477_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
vg0613452440 1.06E-08 NA mr1536_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
vg0613452440 NA 2.69E-09 mr1536_2 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
vg0613452440 NA 2.52E-08 mr1660_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