| Variant ID: vg1105974434 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974434 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGG[C/T]
TCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGA
TCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGA[G/A]
CCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCG
| 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 | 40.20% | 0.20% | 5.25% | 54.40% | NA |
| All Indica | 2759 | 29.90% | 0.30% | 3.62% | 66.11% | NA |
| All Japonica | 1512 | 62.20% | 0.00% | 8.40% | 29.37% | NA |
| Aus | 269 | 16.40% | 0.00% | 2.60% | 81.04% | NA |
| Indica I | 595 | 32.30% | 0.30% | 7.06% | 60.34% | NA |
| Indica II | 465 | 21.50% | 0.60% | 3.66% | 74.19% | NA |
| Indica III | 913 | 29.80% | 0.30% | 0.77% | 69.11% | NA |
| Indica Intermediate | 786 | 33.30% | 0.10% | 4.33% | 62.21% | NA |
| Temperate Japonica | 767 | 57.00% | 0.00% | 11.21% | 31.81% | NA |
| Tropical Japonica | 504 | 65.30% | 0.00% | 4.56% | 30.16% | NA |
| Japonica Intermediate | 241 | 72.60% | 0.00% | 7.47% | 19.92% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 12.50% | 47.92% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 2.22% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974434 | C -> T | LOC_Os11g10840.1 | missense_variant ; p.Leu39Phe; MODERATE | synonymous_codon | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974434 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |