| Variant ID: vg0614963112 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14963112 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGTAATAAATGTTCATAAGCGAATTACTAACACATATTAAACAAGAGTACAAACAAACAAAAGTGTTTAGTCCGAACACTCATCACGATAACATTATGAT[A/G]
CAACACCGAATAGTTCGCAATACTACTAGTACAACAATAGTCGGAGGTACTCATTACAACAAGATTGAATTGAAATTACACGATAGAAGTATTTAGTCCG
CGGACTAAATACTTCTATCGTGTAATTTCAATTCAATCTTGTTGTAATGAGTACCTCCGACTATTGTTGTACTAGTAGTATTGCGAACTATTCGGTGTTG[T/C]
ATCATAATGTTATCGTGATGAGTGTTCGGACTAAACACTTTTGTTTGTTTGTACTCTTGTTTAATATGTGTTAGTAATTCGCTTATGAACATTTATTACT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.30% | 5.60% | 6.77% | 58.38% | NA |
| All Indica | 2759 | 2.90% | 7.30% | 3.88% | 85.90% | NA |
| All Japonica | 1512 | 79.70% | 0.80% | 2.45% | 17.06% | NA |
| Aus | 269 | 12.60% | 14.10% | 44.98% | 28.25% | NA |
| Indica I | 595 | 5.00% | 0.80% | 1.85% | 92.27% | NA |
| Indica II | 465 | 1.70% | 1.10% | 1.94% | 95.27% | NA |
| Indica III | 913 | 0.80% | 14.30% | 5.48% | 79.41% | NA |
| Indica Intermediate | 786 | 4.60% | 7.60% | 4.71% | 83.08% | NA |
| Temperate Japonica | 767 | 96.00% | 0.30% | 0.00% | 3.78% | NA |
| Tropical Japonica | 504 | 51.40% | 2.00% | 6.94% | 39.68% | NA |
| Japonica Intermediate | 241 | 87.10% | 0.00% | 0.83% | 12.03% | NA |
| VI/Aromatic | 96 | 39.60% | 8.30% | 39.58% | 12.50% | NA |
| Intermediate | 90 | 27.80% | 5.60% | 18.89% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614963112 | A -> G | LOC_Os06g25580.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.835; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614963112 | A -> DEL | N | N | silent_mutation | Average:4.835; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |