| Variant ID: vg1105974391 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974391 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGG[G/C]
GAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCG
CGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTC[C/G]
CCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.80% | 21.60% | 21.46% | 22.11% | NA |
| All Indica | 2759 | 15.90% | 26.70% | 30.95% | 26.42% | NA |
| All Japonica | 1512 | 68.90% | 14.20% | 1.92% | 15.01% | NA |
| Aus | 269 | 16.40% | 16.00% | 42.38% | 25.28% | NA |
| Indica I | 595 | 35.50% | 8.10% | 28.74% | 27.73% | NA |
| Indica II | 465 | 15.30% | 19.80% | 30.11% | 34.84% | NA |
| Indica III | 913 | 2.80% | 41.30% | 35.93% | 19.93% | NA |
| Indica Intermediate | 786 | 16.50% | 28.10% | 27.35% | 27.99% | NA |
| Temperate Japonica | 767 | 69.60% | 2.90% | 2.22% | 25.29% | NA |
| Tropical Japonica | 504 | 64.90% | 31.50% | 1.98% | 1.59% | NA |
| Japonica Intermediate | 241 | 75.10% | 13.70% | 0.83% | 10.37% | NA |
| VI/Aromatic | 96 | 88.50% | 4.20% | 5.21% | 2.08% | NA |
| Intermediate | 90 | 42.20% | 23.30% | 13.33% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974391 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:24.489; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
| vg1105974391 | G -> C | LOC_Os11g10840.1 | synonymous_variant ; p.Gly24Gly; LOW | synonymous_codon | Average:24.489; most accessible tissue: Callus, score: 34.526 | N | N | N | N |