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Detailed information for vg0100791504:
| Variant ID: vg0100791504 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791504 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTAAAGACAAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTA[A/G]
GAAGATTACAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCCGTGGCAGTTAAGATG
Reverse complement sequence
CATCTTAACTGCCACGGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTGTAATCTTC[T/C]
TAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTTGTCTTTAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.10% | 1.60% | 10.11% | 19.17% | NA |
| All Indica | 2759 | 71.00% | 1.50% | 15.73% | 11.71% | NA |
| All Japonica | 1512 | 74.00% | 1.10% | 1.59% | 23.35% | NA |
| Aus | 269 | 39.40% | 5.20% | 3.72% | 51.67% | NA |
| Indica I | 595 | 82.00% | 0.70% | 14.79% | 2.52% | NA |
| Indica II | 465 | 88.00% | 0.00% | 8.60% | 3.44% | NA |
| Indica III | 913 | 52.40% | 3.40% | 19.72% | 24.53% | NA |
| Indica Intermediate | 786 | 74.40% | 0.90% | 16.03% | 8.65% | NA |
| Temperate Japonica | 767 | 72.20% | 1.30% | 2.87% | 23.60% | NA |
| Tropical Japonica | 504 | 83.10% | 0.40% | 0.40% | 16.07% | NA |
| Japonica Intermediate | 241 | 60.60% | 1.70% | 0.00% | 37.76% | NA |
| VI/Aromatic | 96 | 15.60% | 2.10% | 6.25% | 76.04% | NA |
| Intermediate | 90 | 74.40% | 1.10% | 4.44% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791504 | A -> G | LOC_Os01g02440.1 | missense_variant ; p.Lys260Arg; MODERATE | nonsynonymous_codon ; K260R | Average:52.495; most accessible tissue: Zhenshan97 panicle, score: 67.02 | benign  |
0.766 |
TOLERATED | 0.06 |
| vg0100791504 | A -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:52.495; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |