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Detailed information for vg1218592795:

Variant ID: vg1218592795 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18592795
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGCCCTTGAGAGAATACTCCCAGCCTTGAGGGAGCATGGCAAGTGCCGGTACACTGTATTACTAAGTCTCTCATTGAACATTTGCCGATAGAAGTTT[G/T]
TTAAGACACTTGCCGTAAGCAAAGTATGGTTGCCCGATCTTCTGGCTAGGCTGAAGCCTTTATATGGTGCACCAATGTCTCCATCTTTGTTTGTCACATC

Reverse complement sequence

GATGTGACAAACAAAGATGGAGACATTGGTGCACCATATAAAGGCTTCAGCCTAGCCAGAAGATCGGGCAACCATACTTTGCTTACGGCAAGTGTCTTAA[C/A]
AAACTTCTATCGGCAAATGTTCAATGAGAGACTTAGTAATACAGTGTACCGGCACTTGCCATGCTCCCTCAAGGCTGGGAGTATTCTCTCAAGGGCAATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.60% 13.40% 2.88% 51.14% NA
All Indica  2759 54.90% 3.20% 2.28% 39.62% NA
All Japonica  1512 0.60% 34.20% 0.53% 64.68% NA
Aus  269 0.00% 1.10% 14.50% 84.39% NA
Indica I  595 35.60% 4.40% 2.86% 57.14% NA
Indica II  465 66.70% 4.30% 0.86% 28.17% NA
Indica III  913 59.70% 1.10% 2.52% 36.69% NA
Indica Intermediate  786 57.10% 3.90% 2.42% 36.51% NA
Temperate Japonica  767 0.80% 58.40% 0.78% 40.03% NA
Tropical Japonica  504 0.20% 3.80% 0.20% 95.83% NA
Japonica Intermediate  241 0.80% 20.70% 0.41% 78.01% NA
VI/Aromatic  96 2.10% 2.10% 16.67% 79.17% NA
Intermediate  90 16.70% 24.40% 11.11% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218592795 G -> DEL LOC_Os12g30960.1 N frameshift_variant Average:40.235; most accessible tissue: Callus, score: 68.465 N N N N
vg1218592795 G -> T LOC_Os12g30960.1 missense_variant ; p.Thr42Lys; MODERATE nonsynonymous_codon ; T42K Average:40.235; most accessible tissue: Callus, score: 68.465 unknown unknown TOLERATED 0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218592795 NA 7.21E-07 mr1090 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
vg1218592795 1.44E-09 2.43E-20 mr1457 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
vg1218592795 1.74E-07 1.86E-11 mr1457 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
vg1218592795 7.32E-13 8.57E-51 mr1458 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
vg1218592795 8.95E-10 1.28E-15 mr1458 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
vg1218592795 NA 2.83E-07 mr1090_2 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
vg1218592795 9.53E-12 5.23E-30 mr1457_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
vg1218592795 2.46E-09 4.71E-14 mr1457_2 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
vg1218592795 9.42E-18 2.18E-58 mr1458_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
vg1218592795 2.71E-15 6.28E-21 mr1458_2 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
vg1218592795 NA 2.41E-07 mr1805_2 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