| Variant ID: vg0625222635 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25222635 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTACCGGACCAGCTGGAGGTACGACGTCCACGGCGCTGCGACAGGAGAAGACGCGCATGACCGCACGCATCTTCTCCTGCATCCGGTCGAAGGTCGACCT[C/T]
TGCTCAACGTCAGTCAAGTGCAAACCTCTGTTCAACCTCACCTGGACTGCGGTGATATCGGCACTGATATCCCGTGCCGCATCAGCCTATGCAAGATGGA
TCCATCTTGCATAGGCTGATGCGGCACGGGATATCAGTGCCGATATCACCGCAGTCCAGGTGAGGTTGAACAGAGGTTTGCACTTGACTGACGTTGAGCA[G/A]
AGGTCGACCTTCGACCGGATGCAGGAGAAGATGCGTGCGGTCATGCGCGTCTTCTCCTGTCGCAGCGCCGTGGACGTCGTACCTCCAGCTGGTCCGGTAC
| 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 | 15.60% | 0.40% | 12.53% | 71.54% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 9.42% | 89.53% | NA |
| All Japonica | 1512 | 44.80% | 1.10% | 13.23% | 40.87% | NA |
| Aus | 269 | 4.80% | 0.00% | 27.51% | 67.66% | NA |
| Indica I | 595 | 0.50% | 0.00% | 8.57% | 90.92% | NA |
| Indica II | 465 | 1.50% | 0.00% | 9.25% | 89.25% | NA |
| Indica III | 913 | 0.50% | 0.00% | 8.21% | 91.24% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 11.58% | 86.64% | NA |
| Temperate Japonica | 767 | 70.50% | 1.60% | 4.17% | 23.73% | NA |
| Tropical Japonica | 504 | 8.10% | 0.20% | 26.19% | 65.48% | NA |
| Japonica Intermediate | 241 | 39.40% | 1.70% | 14.94% | 43.98% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 38.54% | 55.21% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 23.33% | 64.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222635 | C -> T | LOC_Os06g42010.1 | synonymous_variant ; p.Gln807Gln; LOW | synonymous_codon | Average:4.838; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0625222635 | C -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.838; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |