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Detailed information for vg0103158278:

Variant ID: vg0103158278 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3158278
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GCTCGCCAGATGAACGAGTTGATGGAGAAGACGTCCCGTTACCTTGCTGAGTTCGGGACGGGTGGTCGCTATCTCCAACTTAACTCTGTGAGTTCGGCGA[C/G]
TGACGAATTGCCGACGCTGGAGCTTCCAAAGTCCACGCCCACTGAACGCCGCAACGCCCGCATGGTGGAGGAGGATCTATTTAGCATCCAAGATTGTTTG

Reverse complement sequence

CAAACAATCTTGGATGCTAAATAGATCCTCCTCCACCATGCGGGCGTTGCGGCGTTCAGTGGGCGTGGACTTTGGAAGCTCCAGCGTCGGCAATTCGTCA[G/C]
TCGCCGAACTCACAGAGTTAAGTTGGAGATAGCGACCACCCGTCCCGAACTCAGCAAGGTAACGGGACGTCTTCTCCATCAACTCGTTCATCTGGCGAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 0.30% 2.01% 4.63% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 78.50% 0.90% 6.22% 14.42% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 85.40% 0.10% 2.74% 11.73% NA
Tropical Japonica  504 70.00% 0.60% 5.36% 24.01% NA
Japonica Intermediate  241 74.30% 3.70% 19.09% 2.90% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 98.90% 0.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103158278 C -> G LOC_Os01g06690.1 missense_variant ; p.Thr285Ser; MODERATE nonsynonymous_codon ; T285S Average:19.294; most accessible tissue: Callus, score: 36.976 unknown unknown DELETERIOUS 0.00
vg0103158278 C -> DEL LOC_Os01g06690.1 N frameshift_variant Average:19.294; most accessible tissue: Callus, score: 36.976 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103158278 NA 1.42E-06 mr1114 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
vg0103158278 NA 7.68E-08 mr1117 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
vg0103158278 NA 4.66E-07 mr1118 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
vg0103158278 7.04E-06 5.07E-09 mr1123 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
vg0103158278 NA 9.97E-06 mr1150 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
vg0103158278 NA 5.77E-07 mr1240 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
vg0103158278 NA 8.52E-09 mr1242 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
vg0103158278 NA 8.09E-08 mr1247 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
vg0103158278 NA 4.63E-07 mr1496 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
vg0103158278 3.47E-07 4.77E-07 mr1682 Jap_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
vg0103158278 NA 3.71E-07 mr1693 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
vg0103158278 NA 1.17E-06 mr1917 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
vg0103158278 NA 8.85E-07 mr1961 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
vg0103158278 NA 5.85E-06 mr1119_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