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Detailed information for vg0135571255:

Variant ID: vg0135571255 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35571255
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGCTTGAAAGATCTGAAGTTTGAGAAAGATAAGCTTTGTAGTGCTTGTCAAGCCGGCAAGCAAGTTGCAGGTTCTCATTCTACTAAGAGTATCATGTC[C/T]
ACATCTAGACCATTGGAGCTCTTGCATATGAATTTGTTTGGCCCAACAACCTATAAGAGCATTGGTGGTAATAGTCATTGTCTTGTGATTGTTGATGATT

Reverse complement sequence

AATCATCAACAATCACAAGACAATGACTATTACCACCAATGCTCTTATAGGTTGTTGGGCCAAACAAATTCATATGCAAGAGCTCCAATGGTCTAGATGT[G/A]
GACATGATACTCTTAGTAGAATGAGAACCTGCAACTTGCTTGCCGGCTTGACAAGCACTACAAAGCTTATCTTTCTCAAACTTCAGATCTTTCAAGCCCA

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 38.60% 10.50% 42.04% 8.89% NA
All Indica  2759 5.40% 17.10% 63.39% 14.10% NA
All Japonica  1512 98.30% 0.20% 1.06% 0.46% NA
Aus  269 16.00% 6.30% 72.49% 5.20% NA
Indica I  595 4.70% 22.70% 54.12% 18.49% NA
Indica II  465 2.20% 12.70% 67.10% 18.06% NA
Indica III  913 7.20% 16.10% 68.78% 7.89% NA
Indica Intermediate  786 5.70% 16.70% 61.96% 15.65% NA
Temperate Japonica  767 98.80% 0.00% 0.91% 0.26% NA
Tropical Japonica  504 97.60% 0.60% 1.19% 0.60% NA
Japonica Intermediate  241 97.90% 0.00% 1.24% 0.83% NA
VI/Aromatic  96 93.80% 0.00% 6.25% 0.00% NA
Intermediate  90 61.10% 4.40% 23.33% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135571255 C -> T LOC_Os01g61490.1 synonymous_variant ; p.Ser778Ser; LOW synonymous_codon Average:9.006; most accessible tissue: Callus, score: 28.266 N N N N
vg0135571255 C -> DEL LOC_Os01g61490.1 N frameshift_variant Average:9.006; most accessible tissue: Callus, score: 28.266 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0135571255 NA 1.95E-22 mr1003 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
vg0135571255 NA 2.97E-21 mr1051 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
vg0135571255 NA 1.52E-24 mr1024_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
vg0135571255 NA 3.32E-08 mr1084_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
vg0135571255 NA 2.05E-07 mr1205_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
vg0135571255 NA 1.23E-06 mr1275_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
vg0135571255 5.22E-06 2.65E-37 mr1571_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
vg0135571255 NA 1.66E-14 mr1575_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
vg0135571255 NA 2.22E-12 mr1781_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
vg0135571255 NA 2.54E-20 mr1922_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