| Variant ID: vg0614962976 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14962976 |
| 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. )
GCTGTGCACCCTCGACTGCTGACAGGAACGAGCGGTGGTTCCTGTCAATCCCACGGTTCAACAGCGCCGGTGTGTCGTACGCCATACCTGCATCAAATAG[G/A]
TTGATCAGAAACATATAAATAATTAGTTCAACATAAGTAATAAATGTTCATAAGCGAATTACTAACACATATTAAACAAGAGTACAAACAAACAAAAGTG
CACTTTTGTTTGTTTGTACTCTTGTTTAATATGTGTTAGTAATTCGCTTATGAACATTTATTACTTATGTTGAACTAATTATTTATATGTTTCTGATCAA[C/T]
CTATTTGATGCAGGTATGGCGTACGACACACCGGCGCTGTTGAACCGTGGGATTGACAGGAACCACCGCTCGTTCCTGTCAGCAGTCGAGGGTGCACAGC
| 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 | 35.30% | 0.10% | 3.87% | 60.73% | NA |
| All Indica | 2759 | 4.20% | 0.00% | 4.71% | 91.08% | NA |
| All Japonica | 1512 | 82.70% | 0.20% | 1.85% | 15.21% | NA |
| Aus | 269 | 72.90% | 0.00% | 2.60% | 24.54% | NA |
| Indica I | 595 | 5.40% | 0.00% | 1.51% | 93.11% | NA |
| Indica II | 465 | 1.90% | 0.00% | 1.29% | 96.77% | NA |
| Indica III | 913 | 1.80% | 0.00% | 7.78% | 90.47% | NA |
| Indica Intermediate | 786 | 7.50% | 0.00% | 5.60% | 86.90% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.39% | 2.74% | NA |
| Tropical Japonica | 504 | 59.70% | 0.20% | 3.37% | 36.71% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.80% | 3.32% | 9.96% | NA |
| VI/Aromatic | 96 | 68.80% | 0.00% | 12.50% | 18.75% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 6.67% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614962976 | G -> A | LOC_Os06g25580.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.104; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0614962976 | G -> DEL | N | N | silent_mutation | Average:5.104; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |