| Variant ID: vg0807400180 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7400180 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTGTTCTAATATTATTTGAGTTTTAATATAAGATTACTTTATTTGTAATTAGACTTAGTATGTATAATTATTGACTACGGAATTGGGGCGACAAGTAGCA[A/G]
TTGACTATTGTAGTCTTAATTAGACTTAGCATATACGCACGAAACACTTAGCATAGATGACTATTTTAGTCTTAGCATGTAATATTATTGGAGTTTTAAT
ATTAAAACTCCAATAATATTACATGCTAAGACTAAAATAGTCATCTATGCTAAGTGTTTCGTGCGTATATGCTAAGTCTAATTAAGACTACAATAGTCAA[T/C]
TGCTACTTGTCGCCCCAATTCCGTAGTCAATAATTATACATACTAAGTCTAATTACAAATAAAGTAATCTTATATTAAAACTCAAATAATATTAGAACAC
| 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 | 35.80% | 0.10% | 3.75% | 60.39% | NA |
| All Indica | 2759 | 15.30% | 0.00% | 4.71% | 79.99% | NA |
| All Japonica | 1512 | 80.40% | 0.30% | 1.72% | 17.59% | NA |
| Aus | 269 | 3.30% | 0.00% | 5.20% | 91.45% | NA |
| Indica I | 595 | 35.60% | 0.00% | 4.20% | 60.17% | NA |
| Indica II | 465 | 16.10% | 0.00% | 7.74% | 76.13% | NA |
| Indica III | 913 | 1.90% | 0.00% | 2.52% | 95.62% | NA |
| Indica Intermediate | 786 | 15.00% | 0.00% | 5.85% | 79.13% | NA |
| Temperate Japonica | 767 | 66.80% | 0.00% | 2.09% | 31.16% | NA |
| Tropical Japonica | 504 | 95.60% | 0.40% | 1.59% | 2.38% | NA |
| Japonica Intermediate | 241 | 91.70% | 1.20% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 4.44% | 51.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807400180 | A -> G | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0807400180 | A -> DEL | N | N | silent_mutation | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |