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Detailed information for vg1218047368:

Variant ID: vg1218047368 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18047368
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGTGTGTACCTTGCCCCATTCGACCATACGACTTAATTCAGCTGCAGAAGAACGAAAAGTCCCATCACCATTATCATGCACCACCCACTTCCATCTAC[C/T]
AGGTATGAACCTCTCCAACTCAGAAATAATAGAACTTACAGACATCTGTCCTTTAGTGACCTTAACCATAGCCGCTTTAGGCTCATGCTTAACCCTCATT

Reverse complement sequence

AATGAGGGTTAAGCATGAGCCTAAAGCGGCTATGGTTAAGGTCACTAAAGGACAGATGTCTGTAAGTTCTATTATTTCTGAGTTGGAGAGGTTCATACCT[G/A]
GTAGATGGAAGTGGGTGGTGCATGATAATGGTGATGGGACTTTTCGTTCTTCTGCAGCTGAATTAAGTCGTATGGTCGAATGGGGCAAGGTACACACTAA

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 93.00% 6.60% 0.00% 0.42% NA
All Indica  2759 88.20% 11.10% 0.00% 0.72% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 77.60% 21.90% 0.00% 0.43% NA
Indica III  913 90.70% 7.40% 0.00% 1.86% NA
Indica Intermediate  786 88.00% 11.80% 0.00% 0.13% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg1218047368 C -> DEL LOC_Os12g30120.1 N frameshift_variant Average:36.792; most accessible tissue: Minghui63 young leaf, score: 65.161 N N N N
vg1218047368 C -> T LOC_Os12g30120.1 missense_variant ; p.Gly165Ser; MODERATE nonsynonymous_codon ; G165S Average:36.792; most accessible tissue: Minghui63 young leaf, score: 65.161 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218047368 NA 5.39E-06 mr1006 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
vg1218047368 NA 4.78E-06 mr1030 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
vg1218047368 NA 1.05E-06 mr1268 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
vg1218047368 NA 4.21E-06 mr1268 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
vg1218047368 9.38E-06 9.69E-07 mr1321 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
vg1218047368 NA 8.92E-07 mr1371 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
vg1218047368 NA 1.14E-06 mr1371 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
vg1218047368 8.75E-06 NA mr1519 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
vg1218047368 2.43E-06 1.82E-06 mr1545 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
vg1218047368 1.41E-06 1.41E-06 mr1545 Ind_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
vg1218047368 NA 1.67E-06 mr1621 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
vg1218047368 8.35E-06 2.81E-06 mr1621 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
vg1218047368 NA 8.05E-06 mr1749 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
vg1218047368 NA 9.27E-07 mr1761 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
vg1218047368 NA 1.23E-08 mr1769 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
vg1218047368 NA 1.11E-07 mr1951 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