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Detailed information for vg0601059760:

Variant ID: vg0601059760 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 1059760
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTTTATCTCCTATTCTTTTTAATATAGTAGCTGACATGCTTACTCTATTGATTAAGAGGGCTAAAGAGGCGGGACTCTTGAATGGGGTTATTCCTCAT[T/C]
TTGTTGATGATGGTTTGTCTATCTTGCAATACGCAAATGATACTATTATCTTCTTGGAACATGACTTGCAACAGGCAAAGAATTTGAAACTGATTTTATC

Reverse complement sequence

GATAAAATCAGTTTCAAATTCTTTGCCTGTTGCAAGTCATGTTCCAAGAAGATAATAGTATCATTTGCGTATTGCAAGATAGACAAACCATCATCAACAA[A/G]
ATGAGGAATAACCCCATTCAAGAGTCCCGCCTCTTTAGCCCTCTTAATCAATAGAGTAAGCATGTCAGCTACTATATTAAAAAGAATAGGAGATAAAGGA

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 56.50% 33.60% 6.88% 3.00% NA
All Indica  2759 79.60% 11.60% 8.81% 0.04% NA
All Japonica  1512 10.00% 80.80% 0.86% 8.33% NA
Aus  269 92.60% 1.10% 5.58% 0.74% NA
Indica I  595 96.60% 2.50% 0.84% 0.00% NA
Indica II  465 48.80% 44.10% 7.10% 0.00% NA
Indica III  913 85.30% 0.90% 13.80% 0.00% NA
Indica Intermediate  786 78.20% 11.60% 10.05% 0.13% NA
Temperate Japonica  767 0.30% 92.70% 0.00% 7.04% NA
Tropical Japonica  504 28.00% 56.70% 1.79% 13.49% NA
Japonica Intermediate  241 3.30% 93.40% 1.66% 1.66% NA
VI/Aromatic  96 38.50% 4.20% 45.83% 11.46% NA
Intermediate  90 41.10% 45.60% 11.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0601059760 T -> C LOC_Os06g02880.1 missense_variant ; p.Phe711Leu; MODERATE nonsynonymous_codon ; F711L Average:25.634; most accessible tissue: Minghui63 root, score: 41.911 unknown unknown TOLERATED 1.00
vg0601059760 T -> DEL LOC_Os06g02880.1 N frameshift_variant Average:25.634; most accessible tissue: Minghui63 root, score: 41.911 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601059760 NA 1.59E-11 mr1069 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
vg0601059760 NA 1.95E-43 mr1141 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
vg0601059760 NA 6.77E-18 mr1141 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
vg0601059760 NA 5.47E-17 mr1143 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
vg0601059760 NA 3.18E-13 mr1149 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
vg0601059760 NA 2.11E-15 mr1167 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
vg0601059760 NA 1.28E-07 mr1183 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
vg0601059760 NA 1.08E-11 mr1277 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
vg0601059760 NA 4.01E-10 mr1282 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
vg0601059760 NA 9.32E-17 mr1308 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
vg0601059760 NA 2.45E-09 mr1399 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
vg0601059760 NA 3.67E-13 mr1441 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
vg0601059760 NA 1.19E-06 mr1503 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
vg0601059760 NA 1.95E-14 mr1535 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
vg0601059760 NA 1.12E-09 mr1658 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
vg0601059760 NA 5.05E-15 mr1675 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
vg0601059760 NA 2.99E-15 mr1726 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
vg0601059760 NA 2.90E-25 mr1805 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
vg0601059760 NA 1.39E-15 mr1969 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
vg0601059760 NA 5.53E-18 mr1995 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
vg0601059760 4.93E-07 NA mr1039_2 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
vg0601059760 NA 1.10E-18 mr1141_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
vg0601059760 NA 3.66E-07 mr1149_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
vg0601059760 NA 1.06E-15 mr1277_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
vg0601059760 NA 3.96E-10 mr1399_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
vg0601059760 NA 1.67E-07 mr1441_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
vg0601059760 NA 1.22E-07 mr1654_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
vg0601059760 NA 1.45E-06 mr1754_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
vg0601059760 NA 1.99E-42 mr1805_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
vg0601059760 NA 1.17E-07 mr1830_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