| Variant ID: vg0601047105 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1047105 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTCCACGATGGATTGCTTCGCCTCCTCCGGCACGGCCGCCGCCGGCAGCTTCAGCGGGAGCCTGCAGAACCAGAGCACGGAGTACTGCTTGACACGGAGG[T/A]
AATTGCGGCGGCTCATCCTGTTCGTCACCCACTGGACGCCGCGGATGGCGGAGCGGCGGAGCCGGCTCGGCGGCTTGACGGCGTAGTCGCAGACCATGGA
TCCATGGTCTGCGACTACGCCGTCAAGCCGCCGAGCCGGCTCCGCCGCTCCGCCATCCGCGGCGTCCAGTGGGTGACGAACAGGATGAGCCGCCGCAATT[A/T]
CCTCCGTGTCAAGCAGTACTCCGTGCTCTGGTTCTGCAGGCTCCCGCTGAAGCTGCCGGCGGCGGCCGTGCCGGAGGAGGCGAAGCAATCCATCGTGGAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.30% | 3.10% | 15.13% | 0.49% | NA |
| All Indica | 2759 | 76.10% | 5.00% | 18.41% | 0.47% | NA |
| All Japonica | 1512 | 95.40% | 0.20% | 4.10% | 0.26% | NA |
| Aus | 269 | 79.90% | 0.70% | 19.33% | 0.00% | NA |
| Indica I | 595 | 96.00% | 1.00% | 2.86% | 0.17% | NA |
| Indica II | 465 | 86.20% | 3.40% | 10.32% | 0.00% | NA |
| Indica III | 913 | 60.00% | 8.20% | 31.22% | 0.55% | NA |
| Indica Intermediate | 786 | 73.70% | 5.30% | 20.10% | 0.89% | NA |
| Temperate Japonica | 767 | 92.80% | 0.10% | 6.52% | 0.52% | NA |
| Tropical Japonica | 504 | 98.60% | 0.40% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 0.00% | 83.33% | 5.21% | NA |
| Intermediate | 90 | 82.20% | 2.20% | 14.44% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601047105 | T -> A | LOC_Os06g02850.1 | missense_variant ; p.Tyr499Phe; MODERATE | inframe_variant | Average:42.239; most accessible tissue: Minghui63 young leaf, score: 72.408 | N | N | N | N |
| vg0601047105 | T -> A | LOC_Os06g02850.1 | missense_variant ; p.Tyr499Phe; MODERATE | nonsynonymous_codon ; Y499F | Average:42.239; most accessible tissue: Minghui63 young leaf, score: 72.408 | unknown | unknown | TOLERATED | 0.70 |
| vg0601047105 | T -> DEL | LOC_Os06g02850.1 | N | frameshift_variant | Average:42.239; most accessible tissue: Minghui63 young leaf, score: 72.408 | N | N | N | N |