| Variant ID: vg0128724263 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724263 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTCGCACGTCTGTCCTTC[T/C]
TCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCACACCGGCTCCGGCTA
TAGCCGGAGCCGGTGTGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGA[A/G]
GAAGGACAGACGTGCGACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.00% | 1.50% | 4.46% | 27.08% | NA |
| All Indica | 2759 | 58.70% | 0.80% | 2.65% | 37.84% | NA |
| All Japonica | 1512 | 87.00% | 0.80% | 1.12% | 11.04% | NA |
| Aus | 269 | 46.50% | 9.70% | 40.52% | 3.35% | NA |
| Indica I | 595 | 51.10% | 0.20% | 2.02% | 46.72% | NA |
| Indica II | 465 | 52.50% | 0.20% | 1.08% | 46.24% | NA |
| Indica III | 913 | 68.30% | 1.00% | 2.74% | 27.93% | NA |
| Indica Intermediate | 786 | 56.90% | 1.50% | 3.94% | 37.66% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 64.70% | 2.40% | 3.17% | 29.76% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 44.80% | 2.10% | 10.42% | 42.71% | NA |
| Intermediate | 90 | 68.90% | 7.80% | 2.22% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724263 | T -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:13.416; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg0128724263 | T -> C | LOC_Os01g49990.1 | synonymous_variant ; p.Ser52Ser; LOW | synonymous_codon | Average:13.416; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |