Search for Variation information by Variation ID:
Detailed information for vg0143001336:
| Variant ID: vg0143001336 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 43001336 |
| 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: 272. )
Flanking Sequence (100 bp) in Reference Genome:
GGGACCTCGTCGCCTGTGATCATCCGCTGCCTCGGGGTGGCGGGGGCGGAGGCGCCAAGCCTCTCGTCGCCACCCTCGGGCTTGGACGCAGCGGCGAGGT[G/A]
GTCCGCGCGCTGCTCCAGACAAGCGAGCGCGACTTTGAGGTCGCCATGGACAGAGATGGGGCCACCGGGGCCCGGCATCTTCATCTGTAGGTAGGCGTAG
Reverse complement sequence
CTACGCCTACCTACAGATGAAGATGCCGGGCCCCGGTGGCCCCATCTCTGTCCATGGCGACCTCAAAGTCGCGCTCGCTTGTCTGGAGCAGCGCGCGGAC[C/T]
ACCTCGCCGCTGCGTCCAAGCCCGAGGGTGGCGACGAGAGGCTTGGCGCCTCCGCCCCCGCCACCCCGAGGCAGCGGATGATCACAGGCGACGAGGTCCC
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 | 9.00% | 0.20% | 10.58% | 80.24% | NA |
| All Indica | 2759 | 3.20% | 0.20% | 11.82% | 84.78% | NA |
| All Japonica | 1512 | 20.60% | 0.10% | 3.51% | 75.79% | NA |
| Aus | 269 | 3.00% | 0.00% | 31.97% | 65.06% | NA |
| Indica I | 595 | 4.70% | 0.00% | 6.39% | 88.91% | NA |
| Indica II | 465 | 1.50% | 0.60% | 4.52% | 93.33% | NA |
| Indica III | 913 | 2.60% | 0.30% | 19.28% | 77.77% | NA |
| Indica Intermediate | 786 | 3.70% | 0.00% | 11.58% | 84.73% | NA |
| Temperate Japonica | 767 | 38.50% | 0.00% | 1.04% | 60.50% | NA |
| Tropical Japonica | 504 | 1.40% | 0.40% | 7.14% | 91.07% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 3.73% | 92.53% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 22.92% | 72.92% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 14.44% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0143001336 | G -> A | LOC_Os01g74230.1 | missense_variant ; p.His580Tyr; MODERATE | nonsynonymous_codon ; H580Y | Average:15.231; most accessible tissue: Zhenshan97 panicle, score: 32.308 | benign  |
1.317 |
DELETERIOUS | 0.02 |
| vg0143001336 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:15.231; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |