| Variant ID: vg0139512481 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39512481 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTGGTTTCTCCTTGTCTTTAGGACAATGCTTGTAGGTGTGCCCATGTTCATTGTATTTGCTGCAACGCTTCACCCTGCCAGCCTCCGACTCGTCCATAT[T/C]
GTTGCGGATGCGACGAGTCCTCCTCCTTCCAGCCTTGCCTCGGAGCTTCGATGGGTCAGGAATATTGAGTACTTCATCGTTAGTCTCTGTGAACTCCCCA
TGGGGAGTTCACAGAGACTAACGATGAAGTACTCAATATTCCTGACCCATCGAAGCTCCGAGGCAAGGCTGGAAGGAGGAGGACTCGTCGCATCCGCAAC[A/G]
ATATGGACGAGTCGGAGGCTGGCAGGGTGAAGCGTTGCAGCAAATACAATGAACATGGGCACACCTACAAGCATTGTCCTAAAGACAAGGAGAAACCAAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.40% | 1.50% | 1.67% | 70.40% | NA |
| All Indica | 2759 | 2.90% | 1.30% | 2.17% | 93.66% | NA |
| All Japonica | 1512 | 74.50% | 0.30% | 0.07% | 25.13% | NA |
| Aus | 269 | 0.70% | 2.20% | 4.83% | 92.19% | NA |
| Indica I | 595 | 3.70% | 0.20% | 1.34% | 94.79% | NA |
| Indica II | 465 | 3.90% | 0.00% | 2.80% | 93.33% | NA |
| Indica III | 913 | 0.80% | 1.20% | 1.20% | 96.82% | NA |
| Indica Intermediate | 786 | 4.10% | 3.10% | 3.56% | 89.31% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.13% | 2.61% | NA |
| Tropical Japonica | 504 | 52.40% | 0.00% | 0.00% | 47.62% | NA |
| Japonica Intermediate | 241 | 48.50% | 1.70% | 0.00% | 49.79% | NA |
| VI/Aromatic | 96 | 2.10% | 24.00% | 4.17% | 69.79% | NA |
| Intermediate | 90 | 41.10% | 4.40% | 1.11% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139512481 | T -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:9.153; most accessible tissue: Zhenshan97 root, score: 18.731 | N | N | N | N |
| vg0139512481 | T -> C | LOC_Os01g67990.1 | missense_variant ; p.Asn805Asp; MODERATE | nonsynonymous_codon | Average:9.153; most accessible tissue: Zhenshan97 root, score: 18.731 | unknown | unknown | TOLERATED | 1.00 |