| Variant ID: vg0719561643 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19561643 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTTGTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAGACATTTGGCGATTTATTGAAACTCATCAAGAACATTCTTCCGGGGGGAAACAAATTGCC[C/G]
GAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCATAAGATTCACGCATGTCCGAACGATTGTATCCTATATCGCGGTGAGG
CCTCACCGCGATATAGGATACAATCGTTCGGACATGCGTGAATCTTATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTC[G/C]
GGCAATTTGTTTCCCCCCGGAAGAATGTTCTTGATGAGTTTCAATAAATCGCCAAATGTCTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAACAACT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.50% | 0.30% | 34.17% | 62.95% | NA |
| All Indica | 2759 | 1.50% | 0.10% | 20.84% | 77.60% | NA |
| All Japonica | 1512 | 0.10% | 0.90% | 54.63% | 44.38% | NA |
| Aus | 269 | 27.50% | 0.00% | 69.89% | 2.60% | NA |
| Indica I | 595 | 0.00% | 0.00% | 6.89% | 93.11% | NA |
| Indica II | 465 | 0.40% | 0.20% | 11.40% | 87.96% | NA |
| Indica III | 913 | 2.40% | 0.00% | 36.69% | 60.90% | NA |
| Indica Intermediate | 786 | 2.20% | 0.10% | 18.58% | 79.13% | NA |
| Temperate Japonica | 767 | 0.00% | 0.90% | 60.37% | 38.72% | NA |
| Tropical Japonica | 504 | 0.00% | 0.60% | 48.81% | 50.60% | NA |
| Japonica Intermediate | 241 | 0.80% | 1.20% | 48.55% | 49.38% | NA |
| VI/Aromatic | 96 | 1.00% | 1.00% | 4.17% | 93.75% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 24.44% | 73.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561643 | C -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719561643 | C -> G | LOC_Os07g32740.1 | synonymous_variant ; p.Pro200Pro; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |