| Variant ID: vg0319757473 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757473 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATAGTGAGCCAAACGATAGAACTCGTGCAGGTACTTTGTGACGGTCAAATCTGCTTGCTTCAGATAGCGAAACTCTCGTTTTCTTAATGTGATCATTCC[T/C]
GCGGGAACATGTGATCTCCTGAATACAGATGAAAACTCGTTCCAGGTGATGGTATGTCCTTCTGGCTGTGATGCTTCGTAGCTATCCCACCACTCTGAAG
CTTCAGAGTGGTGGGATAGCTACGAAGCATCACAGCCAGAAGGACATACCATCACCTGGAACGAGTTTTCATCTGTATTCAGGAGATCACATGTTCCCGC[A/G]
GGAATGATCACATTAAGAAAACGAGAGTTTCGCTATCTGAAGCAAGCAGATTTGACCGTCACAAAGTACCTGCACGAGTTCTATCGTTTGGCTCACTATG
| 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 | 33.00% | 0.30% | 2.58% | 64.09% | NA |
| All Indica | 2759 | 5.70% | 0.40% | 2.50% | 91.41% | NA |
| All Japonica | 1512 | 83.20% | 0.10% | 2.45% | 14.22% | NA |
| Aus | 269 | 10.80% | 0.40% | 1.86% | 86.99% | NA |
| Indica I | 595 | 1.80% | 0.70% | 1.01% | 96.47% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.94% | 92.26% | NA |
| Indica III | 913 | 7.60% | 0.30% | 3.18% | 88.94% | NA |
| Indica Intermediate | 786 | 6.20% | 0.60% | 3.18% | 89.95% | NA |
| Temperate Japonica | 767 | 93.90% | 0.10% | 1.43% | 4.56% | NA |
| Tropical Japonica | 504 | 66.10% | 0.00% | 3.17% | 30.75% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.40% | 4.15% | 10.37% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 5.21% | 20.83% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 6.67% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757473 | T -> C | LOC_Os03g35670.1 | synonymous_variant ; p.Ala517Ala; LOW | synonymous_codon | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |
| vg0319757473 | T -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:6.461; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |