| Variant ID: vg0725814696 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25814696 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCATAACCAGTCGGCAACGGAAGACGATGATGTCCATCAGTAGTGGTAGCTGTATAAACCAGACGTAGAGGTGAGGGCACTAGTCAGCAGTAGACGAGAC[G/A]
ACCGGTCGGTGAAGACGTAGACGCCCAACAACGGCGGCATAAAGGCCAGCCGTGCAGGCGGAAACACCAGTCGGCGGCGGTCGAGGCGGCCGGTCGGTGA
TCACCGACCGGCCGCCTCGACCGCCGCCGACTGGTGTTTCCGCCTGCACGGCTGGCCTTTATGCCGCCGTTGTTGGGCGTCTACGTCTTCACCGACCGGT[C/T]
GTCTCGTCTACTGCTGACTAGTGCCCTCACCTCTACGTCTGGTTTATACAGCTACCACTACTGATGGACATCATCGTCTTCCGTTGCCGACTGGTTATGC
| 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 | 18.50% | 0.10% | 9.14% | 72.26% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 2.83% | 94.89% | NA |
| All Japonica | 1512 | 48.70% | 0.10% | 17.06% | 34.19% | NA |
| Aus | 269 | 3.30% | 0.40% | 23.05% | 73.23% | NA |
| Indica I | 595 | 1.00% | 0.00% | 2.02% | 96.97% | NA |
| Indica II | 465 | 3.70% | 0.20% | 2.80% | 93.33% | NA |
| Indica III | 913 | 1.40% | 0.20% | 2.74% | 95.62% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 3.56% | 93.38% | NA |
| Temperate Japonica | 767 | 56.50% | 0.10% | 17.73% | 25.68% | NA |
| Tropical Japonica | 504 | 31.00% | 0.00% | 16.87% | 52.18% | NA |
| Japonica Intermediate | 241 | 61.00% | 0.00% | 15.35% | 23.65% | NA |
| VI/Aromatic | 96 | 41.70% | 0.00% | 25.00% | 33.33% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 11.11% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725814696 | G -> DEL | LOC_Os07g43080.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0725814696 | G -> A | LOC_Os07g43080.1 | missense_variant ; p.Ser221Leu; MODERATE | nonsynonymous_codon ; S221L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.67 |