Search for Variation information by Variation ID:
Detailed information for vg0127445588:
| Variant ID: vg0127445588 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 27445588 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 245. )
Flanking Sequence (100 bp) in Reference Genome:
CCACAATACGATTGGGATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGACTTTGCCTTGGTTGCAGGCAGTCCCTCGAGTAATGCCCTGGTTC[T/A]
TTGCAGTTGTAACAAATCAACGTCTTCTTTACTGAGCTGTCCATCTGGGGACGATCATTTTGACTTGGAGTTGGAATTGGTGGTTGGGAATCCTTGCTAA
Reverse complement sequence
TTAGCAAGGATTCCCAACCACCAATTCCAACTCCAAGTCAAAATGATCGTCCCCAGATGGACAGCTCAGTAAAGAAGACGTTGATTTGTTACAACTGCAA[A/T]
GAACCAGGGCATTACTCGAGGGACTGCCTGCAACCAAGGCAAAGTCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATCCCAATCGTATTGTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.10% | 8.70% | 5.86% | 30.30% | NA |
| All Indica | 2759 | 42.50% | 1.40% | 6.49% | 49.62% | NA |
| All Japonica | 1512 | 77.40% | 16.70% | 5.49% | 0.40% | NA |
| Aus | 269 | 39.40% | 39.40% | 3.72% | 17.47% | NA |
| Indica I | 595 | 22.40% | 0.30% | 6.55% | 70.76% | NA |
| Indica II | 465 | 35.70% | 2.40% | 5.38% | 56.56% | NA |
| Indica III | 913 | 52.70% | 0.40% | 7.56% | 39.32% | NA |
| Indica Intermediate | 786 | 49.90% | 2.80% | 5.85% | 41.48% | NA |
| Temperate Japonica | 767 | 95.60% | 2.90% | 1.43% | 0.13% | NA |
| Tropical Japonica | 504 | 47.80% | 40.10% | 11.31% | 0.79% | NA |
| Japonica Intermediate | 241 | 81.70% | 11.60% | 6.22% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 16.70% | 4.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0127445588 | T -> A | LOC_Os01g47960.1 | missense_variant ; p.Lys451Asn; MODERATE | nonsynonymous_codon ; K451N | Average:4.894; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.341 |
TOLERATED | 0.83 |
| vg0127445588 | T -> DEL | LOC_Os01g47960.1 | N | frameshift_variant | Average:4.894; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0127445588 | NA | 8.12E-07 | mr1543 | 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 |
| vg0127445588 | NA | 9.16E-07 | mr1671 | 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 |
| vg0127445588 | NA | 7.05E-10 | mr1047_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 |
| vg0127445588 | NA | 3.62E-10 | mr1543_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 |
| vg0127445588 | NA | 7.84E-09 | mr1642_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 |
| vg0127445588 | NA | 8.13E-07 | mr1696_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 |
| vg0127445588 | NA | 2.12E-07 | mr1819_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 |