Search for Variation information by Variation ID:
Detailed information for vg0601268839:
| Variant ID: vg0601268839 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1268839 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
CTCCGCTTCGGCGGGAGGATCTTTCGACGTGGAGTCATCTTGGGTTACAGCCACTGCGTTCTCGTTTCTGGTCCTAGACGGCCCAGCTGAGATCGGCGTC[G/A]
TGGTGTAAACCGGAAAGACAATCTCGCTGACTTGAGTCGACGCAAGCGTCGTTGAGGCAGGAAGCCCGTAGTTAAGGTTGGCGTTGGCGCTGTTGTCGAC
Reverse complement sequence
GTCGACAACAGCGCCAACGCCAACCTTAACTACGGGCTTCCTGCCTCAACGACGCTTGCGTCGACTCAAGTCAGCGAGATTGTCTTTCCGGTTTACACCA[C/T]
GACGCCGATCTCAGCTGGGCCGTCTAGGACCAGAAACGAGAACGCAGTGGCTGTAACCCAAGATGACTCCACGTCGAAAGATCCTCCCGCCGAAGCGGAG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 89.90% | 10.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 79.20% | 20.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 81.80% | 18.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 51.00% | 49.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0601268839 | G -> A | LOC_Os06g03320.1 | missense_variant ; p.Thr80Met; MODERATE | nonsynonymous_codon ; T80M | Average:48.891; most accessible tissue: Minghui63 young leaf, score: 72.408 | probably damaging  |
2.771 |
DELETERIOUS | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601268839 | 4.38E-06 | 4.38E-06 | mr1240 | 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 |