| Variant ID: vg0721993779 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993779 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 400. )
TTCAATTCAGCCAAAAGATTTTTCAACCATAACAATTCACTCAAGCTCATCGACATTGACCTGTATTCCGCCTCAGCAGTCGAGCGAGACACAACTGATT[G/A]
TTTCTTGCTCCTCCAAGATACCAAATTGCCACCAATAAATACACAGTAGCCTGATGTTGACCTCCTATCATCAAGACAACTGCCCCAATCTGCATCACAA
TTGTGATGCAGATTGGGGCAGTTGTCTTGATGATAGGAGGTCAACATCAGGCTACTGTGTATTTATTGGTGGCAATTTGGTATCTTGGAGGAGCAAGAAA[C/T]
AATCAGTTGTGTCTCGCTCGACTGCTGAGGCGGAATACAGGTCAATGTCGATGAGCTTGAGTGAATTGTTATGGTTGAAAAATCTTTTGGCTGAATTGAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.00% | 0.10% | 1.27% | 1.67% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.14% | 0.04% | NA |
| All Japonica | 1512 | 92.50% | 0.00% | 2.38% | 5.16% | NA |
| Aus | 269 | 92.90% | 0.00% | 7.06% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.00% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.65% | 2.35% | NA |
| Tropical Japonica | 504 | 89.70% | 0.00% | 4.76% | 5.56% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.00% | 2.90% | 13.28% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993779 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:11.981; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0721993779 | G -> A | LOC_Os07g36710.1 | stop_gained ; p.Gln682*; HIGH | stop_gained | Average:11.981; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |