| Variant ID: vg1007670732 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670732 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAAGTACAAATGGTTCATCGGCGTATCCCACCTTATATAGATCTACTAAAGTGAAACCTTCCTTGTCGGCTTTGACACCAGTGCGTAGATTCACCCAACG[G/A]
CAGCGGAACAAAGGAACCTTGAACTTGACGTAGTTTAGCTCCCATATCTCCTCAATGCGGCCGTAGTATGTGTTTGACCCAACTTGATCCTGGAATGCAT
ATGCATTCCAGGATCAAGTTGGGTCAAACACATACTACGGCCGCATTGAGGAGATATGGGAGCTAAACTACGTCAAGTTCAAGGTTCCTTTGTTCCGCTG[C/T]
CGTTGGGTGAATCTACGCACTGGTGTCAAAGCCGACAAGGAAGGTTTCACTTTAGTAGATCTATATAAGGTGGGATACGCCGATGAACCATTTGTACTTG
| 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 | 49.80% | 24.30% | 17.46% | 8.40% | NA |
| All Indica | 2759 | 79.60% | 7.00% | 10.87% | 2.46% | NA |
| All Japonica | 1512 | 2.20% | 54.40% | 22.69% | 20.70% | NA |
| Aus | 269 | 27.90% | 18.20% | 53.90% | 0.00% | NA |
| Indica I | 595 | 84.20% | 1.80% | 13.78% | 0.17% | NA |
| Indica II | 465 | 82.60% | 4.70% | 8.60% | 4.09% | NA |
| Indica III | 913 | 82.00% | 8.30% | 7.78% | 1.86% | NA |
| Indica Intermediate | 786 | 71.60% | 10.80% | 13.61% | 3.94% | NA |
| Temperate Japonica | 767 | 1.70% | 68.30% | 26.21% | 3.78% | NA |
| Tropical Japonica | 504 | 2.40% | 24.40% | 22.22% | 50.99% | NA |
| Japonica Intermediate | 241 | 3.70% | 72.60% | 12.45% | 11.20% | NA |
| VI/Aromatic | 96 | 13.50% | 59.40% | 16.67% | 10.42% | NA |
| Intermediate | 90 | 38.90% | 31.10% | 23.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670732 | G -> A | LOC_Os10g14130.1 | synonymous_variant ; p.Cys393Cys; LOW | synonymous_codon | Average:9.147; most accessible tissue: Callus, score: 26.336 | N | N | N | N |
| vg1007670732 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:9.147; most accessible tissue: Callus, score: 26.336 | N | N | N | N |