| Variant ID: vg1105974506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974506 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGAC[G/C]
TCTGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATCTGTGCGAGGAGTTGTGCAGCGGTGGAT
ATCCACCGCTGCACAACTCCTCGCACAGATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCAGA[C/G]
GTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACC
| 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 | 95.70% | 0.10% | 2.94% | 1.21% | NA |
| All Indica | 2759 | 94.20% | 0.20% | 4.28% | 1.34% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.33% | 1.26% | NA |
| Aus | 269 | 94.80% | 0.00% | 4.83% | 0.37% | NA |
| Indica I | 595 | 93.40% | 0.00% | 4.71% | 1.85% | NA |
| Indica II | 465 | 92.90% | 0.20% | 4.30% | 2.58% | NA |
| Indica III | 913 | 94.10% | 0.20% | 4.82% | 0.88% | NA |
| Indica Intermediate | 786 | 95.70% | 0.30% | 3.31% | 0.76% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.39% | 2.48% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974506 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:45.682; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974506 | G -> C | LOC_Os11g10840.1 | missense_variant ; p.Val63Leu; MODERATE | nonsynonymous_codon ; V63L | Average:45.682; most accessible tissue: Callus, score: 75.127 | unknown | unknown | TOLERATED | 0.30 |