| Variant ID: vg0128724248 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28724248 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATGCAACGTGGGAGCACGGTTTGTCTGCTGATGACGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGTC[G/A]
CACGTCTGTCCTTCTTCATACAATGACTTCTTTGCAATGGTTGCGATGAAGCCTGGAATGTATCTAGCCGGGACTGGCGTGCTAACTCCAGGAGTTAGCA
TGCTAACTCCTGGAGTTAGCACGCCAGTCCCGGCTAGATACATTCCAGGCTTCATCGCAACCATTGCAAAGAAGTCATTGTATGAAGAAGGACAGACGTG[C/T]
GACATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACGTCATCAGCAGACAAACCGTGCTCCCACGTTGCAT
| 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 | 66.30% | 1.80% | 3.49% | 28.40% | NA |
| All Indica | 2759 | 57.70% | 1.40% | 2.57% | 38.31% | NA |
| All Japonica | 1512 | 86.90% | 0.80% | 0.93% | 11.38% | NA |
| Aus | 269 | 44.60% | 10.00% | 28.62% | 16.73% | NA |
| Indica I | 595 | 49.70% | 0.20% | 1.68% | 48.40% | NA |
| Indica II | 465 | 51.80% | 0.20% | 0.86% | 47.10% | NA |
| Indica III | 913 | 67.90% | 1.80% | 3.18% | 27.16% | NA |
| Indica Intermediate | 786 | 55.50% | 2.50% | 3.56% | 38.42% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 64.30% | 2.40% | 2.58% | 30.75% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 46.90% | 2.10% | 2.08% | 48.96% | NA |
| Intermediate | 90 | 67.80% | 7.80% | 1.11% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128724248 | G -> A | LOC_Os01g49990.1 | synonymous_variant ; p.Ser47Ser; LOW | synonymous_codon | Average:11.799; most accessible tissue: Callus, score: 22.262 | N | N | N | N |
| vg0128724248 | G -> DEL | LOC_Os01g49990.1 | N | frameshift_variant | Average:11.799; most accessible tissue: Callus, score: 22.262 | N | N | N | N |