| Variant ID: vg0128724151 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724151 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCATTCCTCCATTAATGGGCGGAGATTTGCAATGGCCGCTGTCCGAATGACCCTCCGATGGGATGGGTCATACCTACCTCCACTTCGCTGGAAGCAGATG[C/T]
AACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCAC
GTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTT[G/A]
CATCTGCTTCCAGCGAAGTGGAGGTAGGTATGACCCATCCCATCGGAGGGTCATTCGGACAGCGGCCATTGCAAATCTCCGCCCATTAATGGAGGAATGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.30% | 0.00% | 12.02% | 51.65% | NA |
| All Indica | 2759 | 8.10% | 0.00% | 16.85% | 75.03% | NA |
| All Japonica | 1512 | 85.70% | 0.10% | 1.98% | 12.24% | NA |
| Aus | 269 | 48.00% | 0.00% | 17.10% | 34.94% | NA |
| Indica I | 595 | 3.50% | 0.00% | 4.71% | 91.76% | NA |
| Indica II | 465 | 6.20% | 0.00% | 15.05% | 78.71% | NA |
| Indica III | 913 | 9.40% | 0.00% | 26.94% | 63.64% | NA |
| Indica Intermediate | 786 | 11.20% | 0.00% | 15.39% | 73.41% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 61.30% | 0.20% | 5.95% | 32.54% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 20.83% | 60.42% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 7.78% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724151 | C -> T | LOC_Os01g49990.1 | missense_variant ; p.Ala15Val; MODERATE | nonsynonymous_codon ; A15V | Average:9.32; most accessible tissue: Zhenshan97 panicle, score: 20.424 | unknown | unknown | TOLERATED | 0.22 |
| vg0128724151 | C -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:9.32; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |