| Variant ID: vg0725418494 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25418494 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACGGTCTCAATCCATGCACATTGGTAATGGTGACTTGGCTGTCCATAATGGGCGGTCTCTTCAAGACTGCCACGTTACCTGAGCAGCGCACGAATCTGGG[C/G]
GAGCCGATTTGCTTCGCCTGGAGATATGGTGATGGTGCTTTTCTCGGAGCCATCAGAATAGCGTATAGCATCTTCTGGGCCCGAGGGTATCGGGTTTTGG
CCAAAACCCGATACCCTCGGGCCCAGAAGATGCTATACGCTATTCTGATGGCTCCGAGAAAAGCACCATCACCATATCTCCAGGCGAAGCAAATCGGCTC[G/C]
CCCAGATTCGTGCGCTGCTCAGGTAACGTGGCAGTCTTGAAGAGACCGCCCATTATGGACAGCCAAGTCACCATTACCAATGTGCATGGATTGAGACCGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.10% | 0.00% | 4.95% | 73.89% | NA |
| All Indica | 2759 | 1.80% | 0.00% | 3.04% | 95.11% | NA |
| All Japonica | 1512 | 59.90% | 0.10% | 6.35% | 33.66% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 3.20% | 0.00% | 3.53% | 93.28% | NA |
| Indica II | 465 | 1.90% | 0.00% | 2.80% | 95.27% | NA |
| Indica III | 913 | 0.10% | 0.00% | 3.07% | 96.82% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 2.80% | 94.40% | NA |
| Temperate Japonica | 767 | 88.80% | 0.10% | 1.96% | 9.13% | NA |
| Tropical Japonica | 504 | 13.70% | 0.00% | 12.10% | 74.21% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 8.30% | 26.97% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 51.04% | 35.42% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 5.56% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725418494 | C -> DEL | LOC_Os07g42460.1 | N | frameshift_variant | Average:5.976; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0725418494 | C -> G | LOC_Os07g42460.1 | synonymous_variant ; p.Ser683Ser; LOW | synonymous_codon | Average:5.976; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |