| Variant ID: vg0614961452 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14961452 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTAGCTAACACCCAGTCGTCAACGTACTGCTGTACACGTGGAGCCCAAAGTGCGCCTGCTAGCTGTCCCCGTCGAGTCAACCTGTGAAGAGAGGTAAATT[G/A]
TATGGCTCGATGATGTAATTATCATAAAAATTTAGAAATGAACAATCCGAACTCACGAGTGGTCGGCAGGGGGGACGGTCGGCTGCACGTTGCCGGGAAA
TTTCCCGGCAACGTGCAGCCGACCGTCCCCCCTGCCGACCACTCGTGAGTTCGGATTGTTCATTTCTAAATTTTTATGATAATTACATCATCGAGCCATA[C/T]
AATTTACCTCTCTTCACAGGTTGACTCGACGGGGACAGCTAGCAGGCGCACTTTGGGCTCCACGTGTACAGCAGTACGTTGACGACTGGGTGTTAGCTAC
| 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 | 23.20% | 0.20% | 23.55% | 53.03% | NA |
| All Indica | 2759 | 5.10% | 0.30% | 12.72% | 81.81% | NA |
| All Japonica | 1512 | 50.80% | 0.10% | 40.01% | 9.13% | NA |
| Aus | 269 | 55.00% | 0.00% | 24.16% | 20.82% | NA |
| Indica I | 595 | 4.90% | 0.30% | 9.08% | 85.71% | NA |
| Indica II | 465 | 5.80% | 0.40% | 12.04% | 81.72% | NA |
| Indica III | 913 | 3.20% | 0.40% | 13.58% | 82.80% | NA |
| Indica Intermediate | 786 | 7.30% | 0.10% | 14.89% | 77.74% | NA |
| Temperate Japonica | 767 | 46.30% | 0.00% | 51.37% | 2.35% | NA |
| Tropical Japonica | 504 | 50.60% | 0.20% | 28.97% | 20.24% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 26.97% | 7.47% | NA |
| VI/Aromatic | 96 | 19.80% | 0.00% | 59.38% | 20.83% | NA |
| Intermediate | 90 | 21.10% | 1.10% | 38.89% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614961452 | G -> A | LOC_Os06g25580.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.508; most accessible tissue: Callus, score: 15.921 | N | N | N | N |
| vg0614961452 | G -> DEL | N | N | silent_mutation | Average:5.508; most accessible tissue: Callus, score: 15.921 | N | N | N | N |