| Variant ID: vg0306600589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 6600589 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGATGACCAGTGGAACCCAGAGGATCATCTCCCCTCATTCAAAGATGACTCCCTGATACCATATGACGTACCTAGTTGCCACCTGGTTTGATAATTAACA[G/A]
CATCTTGAAAAATTCAGTACATCAAGTGCAAATGTTCAGGCCACTAACTTTTGCAATGTCAATATTAATTTGCAGATATTTATTCCACTACTTCAACCAC
GTGGTTGAAGTAGTGGAATAAATATCTGCAAATTAATATTGACATTGCAAAAGTTAGTGGCCTGAACATTTGCACTTGATGTACTGAATTTTTCAAGATG[C/T]
TGTTAATTATCAAACCAGGTGGCAACTAGGTACGTCATATGGTATCAGGGAGTCATCTTTGAATGAGGGGAGATGATCCTCTGGGTTCCACTGGTCATCA
| 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 | 39.20% | 10.90% | 3.13% | 46.85% | NA |
| All Indica | 2759 | 8.70% | 16.80% | 4.53% | 70.03% | NA |
| All Japonica | 1512 | 96.80% | 0.20% | 0.53% | 2.45% | NA |
| Aus | 269 | 10.80% | 12.60% | 2.60% | 73.98% | NA |
| Indica I | 595 | 1.70% | 29.20% | 2.69% | 66.39% | NA |
| Indica II | 465 | 2.20% | 13.50% | 3.44% | 80.86% | NA |
| Indica III | 913 | 15.70% | 14.60% | 6.13% | 63.64% | NA |
| Indica Intermediate | 786 | 9.70% | 11.80% | 4.71% | 73.79% | NA |
| Temperate Japonica | 767 | 97.10% | 0.10% | 0.65% | 2.09% | NA |
| Tropical Japonica | 504 | 95.40% | 0.40% | 0.60% | 3.57% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 74.00% | 7.30% | 0.00% | 18.75% | NA |
| Intermediate | 90 | 53.30% | 6.70% | 8.89% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0306600589 | G -> A | LOC_Os03g12490.1 | downstream_gene_variant ; 1574.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0306600589 | G -> A | LOC_Os03g12480.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0306600589 | G -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |