| Variant ID: vg0721993814 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993814 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: Unkown |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 386. )
TTCACTCAAGCTCATCGACATTGACCTGTATTCCGCCTCAGCAGTCGAGCGAGACACAACTGATTGTTTCTTGCTCCTCCAAGATACCAAATTGCCACCA[A/T]
TAAATACACAGTAGCCTGATGTTGACCTCCTATCATCAAGACAACTGCCCCAATCTGCATCACAATATCCCTCCACATCTAGGTGTCCATTCTTCTTGAA
TTCAAGAAGAATGGACACCTAGATGTGGAGGGATATTGTGATGCAGATTGGGGCAGTTGTCTTGATGATAGGAGGTCAACATCAGGCTACTGTGTATTTA[T/A]
TGGTGGCAATTTGGTATCTTGGAGGAGCAAGAAACAATCAGTTGTGTCTCGCTCGACTGCTGAGGCGGAATACAGGTCAATGTCGATGAGCTTGAGTGAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 0.00% | 0.78% | 1.63% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.14% | 0.04% | NA |
| All Japonica | 1512 | 94.10% | 0.00% | 0.86% | 5.03% | NA |
| Aus | 269 | 92.90% | 0.00% | 7.06% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.00% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.39% | 2.35% | NA |
| Tropical Japonica | 504 | 92.90% | 0.00% | 1.59% | 5.56% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 0.83% | 12.45% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993814 | A -> T | LOC_Os07g36710.1 | missense_variant ; p.Ile670Asn; MODERATE | N | Average:11.981; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0721993814 | A -> T | LOC_Os07g36720.1 | upstream_gene_variant ; 3836.0bp to feature; MODIFIER | N | Average:11.981; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0721993814 | A -> T | LOC_Os07g36700.1 | downstream_gene_variant ; 2058.0bp to feature; MODIFIER | N | Average:11.981; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |