| Variant ID: vg1007738748 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738748 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTCTGCTGCCGTTGGGGGTGGAGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGCGCCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGC[C/G]
TGTGGGGCTGCCCCTGCGACGGCGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATACCGCGTGGTGAAGGTCAATGTGCTTCAGAGGATCATTCCTGA
TCAGGAATGATCCTCTGAAGCACATTGACCTTCACCACGCGGTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCGCCGTCGCAGGGGCAGCCCCACA[G/C]
GCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGGCGCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACTCCACCCCCAACGGCAGCAGACC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 69.10% | 2.60% | 14.66% | 13.58% | NA |
| All Indica | 2759 | 69.00% | 3.40% | 14.39% | 13.19% | NA |
| All Japonica | 1512 | 67.70% | 0.60% | 13.89% | 17.79% | NA |
| Aus | 269 | 65.80% | 5.90% | 28.25% | 0.00% | NA |
| Indica I | 595 | 62.50% | 0.30% | 18.15% | 18.99% | NA |
| Indica II | 465 | 66.70% | 1.30% | 17.63% | 14.41% | NA |
| Indica III | 913 | 73.50% | 7.30% | 12.16% | 7.01% | NA |
| Indica Intermediate | 786 | 70.00% | 2.50% | 12.21% | 15.27% | NA |
| Temperate Japonica | 767 | 62.70% | 0.80% | 20.34% | 16.17% | NA |
| Tropical Japonica | 504 | 72.80% | 0.60% | 10.12% | 16.47% | NA |
| Japonica Intermediate | 241 | 73.00% | 0.00% | 1.24% | 25.73% | NA |
| VI/Aromatic | 96 | 92.70% | 2.10% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 2.20% | 5.56% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738748 | C -> G | LOC_Os10g14290.1 | missense_variant ; p.Gln254His; MODERATE | nonsynonymous_codon ; Q254P | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.27 |
| vg1007738748 | C -> G | LOC_Os10g14290.1 | missense_variant ; p.Gln254His; MODERATE | nonsynonymous_codon ; Q254R | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.31 |
| vg1007738748 | C -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |