| Variant ID: vg0303700054 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 3700054 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 336. )
ACATACATCTGCATCATTTTCTTTCCCATTTCCCATATGTGATATTCAGTTTCTGATCCAGAACAGAGCTTCACAACTGATATCCTCAACCAATGAATCC[T/A]
TTTCTTTCAGAATGTGATCTCGACTGTCCAAAAGACTGAATTATATCCTTCACACTGCCATCTACAAACGTTTGACCTGCTTCTTTGTTGACACCACTGT
ACAGTGGTGTCAACAAAGAAGCAGGTCAAACGTTTGTAGATGGCAGTGTGAAGGATATAATTCAGTCTTTTGGACAGTCGAGATCACATTCTGAAAGAAA[A/T]
GGATTCATTGGTTGAGGATATCAGTTGTGAAGCTCTGTTCTGGATCAGAAACTGAATATCACATATGGGAAATGGGAAAGAAAATGATGCAGATGTATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.80% | 8.80% | 0.06% | 0.28% | NA |
| All Indica | 2759 | 84.40% | 15.00% | 0.11% | 0.47% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.40% | 13.40% | 0.00% | 0.17% | NA |
| Indica II | 465 | 92.00% | 7.30% | 0.00% | 0.65% | NA |
| Indica III | 913 | 76.90% | 22.20% | 0.33% | 0.55% | NA |
| Indica Intermediate | 786 | 87.20% | 12.30% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0303700054 | T -> A | LOC_Os03g07234.1 | missense_variant ; p.Lys511Asn; MODERATE | nonsynonymous_codon ; K511N | Average:43.528; most accessible tissue: Callus, score: 82.522 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0303700054 | T -> DEL | LOC_Os03g07234.1 | N | frameshift_variant | Average:43.528; most accessible tissue: Callus, score: 82.522 | N | N | N | N |