| Variant ID: vg1105974430 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974430 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTT[T/C]
CGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCA
TGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCG[A/G]
AACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCT
| 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 | 46.50% | 0.20% | 3.39% | 49.94% | NA |
| All Indica | 2759 | 32.50% | 0.40% | 1.78% | 65.31% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 6.02% | 19.44% | NA |
| Aus | 269 | 18.20% | 0.00% | 2.97% | 78.81% | NA |
| Indica I | 595 | 37.60% | 0.30% | 2.69% | 59.33% | NA |
| Indica II | 465 | 22.80% | 0.60% | 2.58% | 73.98% | NA |
| Indica III | 913 | 30.80% | 0.40% | 0.88% | 67.91% | NA |
| Indica Intermediate | 786 | 36.50% | 0.10% | 1.65% | 61.70% | NA |
| Temperate Japonica | 767 | 65.80% | 0.00% | 6.00% | 28.16% | NA |
| Tropical Japonica | 504 | 85.50% | 0.00% | 5.95% | 8.53% | NA |
| Japonica Intermediate | 241 | 79.30% | 0.00% | 6.22% | 14.52% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 9.38% | 20.83% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974430 | T -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974430 | T -> C | LOC_Os11g10840.1 | synonymous_variant ; p.Phe37Phe; LOW | synonymous_codon | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |