| Variant ID: vg0807400176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7400176 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGTAGTGTTCTAATATTATTTGAGTTTTAATATAAGATTACTTTATTTGTAATTAGACTTAGTATGTATAATTATTGACTACGGAATTGGGGCGACAAGT[A/T]
GCAATTGACTATTGTAGTCTTAATTAGACTTAGCATATACGCACGAAACACTTAGCATAGATGACTATTTTAGTCTTAGCATGTAATATTATTGGAGTTT
AAACTCCAATAATATTACATGCTAAGACTAAAATAGTCATCTATGCTAAGTGTTTCGTGCGTATATGCTAAGTCTAATTAAGACTACAATAGTCAATTGC[T/A]
ACTTGTCGCCCCAATTCCGTAGTCAATAATTATACATACTAAGTCTAATTACAAATAAAGTAATCTTATATTAAAACTCAAATAATATTAGAACACTACA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.50% | 0.10% | 3.94% | 60.43% | NA |
| All Indica | 2759 | 15.00% | 0.00% | 5.04% | 79.99% | NA |
| All Japonica | 1512 | 80.40% | 0.30% | 1.59% | 17.72% | NA |
| Aus | 269 | 2.60% | 0.00% | 5.95% | 91.45% | NA |
| Indica I | 595 | 35.30% | 0.00% | 4.54% | 60.17% | NA |
| Indica II | 465 | 14.80% | 0.00% | 9.03% | 76.13% | NA |
| Indica III | 913 | 1.90% | 0.00% | 2.52% | 95.62% | NA |
| Indica Intermediate | 786 | 14.90% | 0.00% | 5.98% | 79.13% | NA |
| Temperate Japonica | 767 | 67.10% | 0.00% | 1.43% | 31.42% | NA |
| Tropical Japonica | 504 | 94.60% | 1.00% | 1.98% | 2.38% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 1.24% | 6.22% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 43.30% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0807400176 | A -> T | LOC_Os08g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0807400176 | A -> DEL | N | N | silent_mutation | Average:4.449; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |