| Variant ID: vg0719561597 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19561597 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TACCCAGGTTGCGAGCAGGAGCACAAAAAGTTGGATACCACTCTGGAGTTGTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAGACATTTGGCGATT[T/G]
ATTGAAACTCATCAAGAACATTCTTCCGGGGGGAAACAAATTGCCCGAGACAACGTACGAGGCTAAGAAGATAGTCTGCCCGTTAGGACTGGAAGTTCAT
ATGAACTTCCAGTCCTAACGGGCAGACTATCTTCTTAGCCTCGTACGTTGTCTCGGGCAATTTGTTTCCCCCCGGAAGAATGTTCTTGATGAGTTTCAAT[A/C]
AATCGCCAAATGTCTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAACAACTCCAGAGTGGTATCCAACTTTTTGTGCTCCTGCTCGCAACCTGGGTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.50% | 2.20% | 22.66% | 53.60% | NA |
| All Indica | 2759 | 4.00% | 1.30% | 26.17% | 68.54% | NA |
| All Japonica | 1512 | 59.10% | 0.10% | 8.86% | 32.01% | NA |
| Aus | 269 | 0.40% | 23.80% | 73.61% | 2.23% | NA |
| Indica I | 595 | 1.50% | 0.00% | 13.11% | 85.38% | NA |
| Indica II | 465 | 2.80% | 0.00% | 15.48% | 81.72% | NA |
| Indica III | 913 | 6.70% | 2.80% | 41.07% | 49.40% | NA |
| Indica Intermediate | 786 | 3.40% | 1.30% | 25.06% | 70.23% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 2.74% | 4.30% | NA |
| Tropical Japonica | 504 | 11.30% | 0.00% | 18.65% | 70.04% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.40% | 7.88% | 40.66% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 13.30% | 2.20% | 14.44% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719561597 | T -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719561597 | T -> G | LOC_Os07g32740.1 | N | stop_gained | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |