| Variant ID: vg1117778239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17778239 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 377. )
TCGCGATGCCGAAGTGGGAGCAGATGGAGGCTAGCTTGATTGAGAGGGGTATCGAACCGGCAACAGCCAATTGGCCGGAACGATCGAAGTTCTGGTACTA[T/C]
GCTCACGGTGGAACGCTCAACCCAGCTGATGGCTCACTGGTCTTCGGCGATCAGATACGAGAGGCTGCGCGACGACTAACAGATGCAGTGGAAGCCTCCT
AGGAGGCTTCCACTGCATCTGTTAGTCGTCGCGCAGCCTCTCGTATCTGATCGCCGAAGACCAGTGAGCCATCAGCTGGGTTGAGCGTTCCACCGTGAGC[A/G]
TAGTACCAGAACTTCGATCGTTCCGGCCAATTGGCTGTTGCCGGTTCGATACCCCTCTCAATCAAGCTAGCCTCCATCTGCTCCCACTTCGGCATCGCGA
| 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 | 0.30% | 0.20% | 3.91% | 95.51% | NA |
| All Indica | 2759 | 0.60% | 0.10% | 4.35% | 95.00% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 2.25% | 97.42% | NA |
| Aus | 269 | 0.00% | 0.40% | 1.86% | 97.77% | NA |
| Indica I | 595 | 0.30% | 0.00% | 2.02% | 97.65% | NA |
| Indica II | 465 | 0.60% | 0.40% | 11.61% | 87.31% | NA |
| Indica III | 913 | 0.70% | 0.00% | 2.52% | 96.82% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 3.94% | 95.42% | NA |
| Temperate Japonica | 767 | 0.00% | 0.40% | 2.87% | 96.74% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 1.79% | 98.02% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 1.24% | 98.34% | NA |
| VI/Aromatic | 96 | 0.00% | 2.10% | 18.75% | 79.17% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 8.89% | 90.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778239 | T -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:12.594; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1117778239 | T -> C | LOC_Os11g30552.1 | synonymous_variant ; p.Tyr397Tyr; LOW | synonymous_codon | Average:12.594; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |