| Variant ID: vg1220960445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960445 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 304. )
CATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCTGAGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAA[T/C]
GAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTGCACTAGATTTTGCTATGTGTATCTATTGAAAACAAAGGATGAG
CTCATCCTTTGTTTTCAATAGATACACATAGCAAAATCTAGTGCAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTC[A/G]
TTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATG
| 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 | 58.30% | 0.60% | 0.66% | 40.52% | NA |
| All Indica | 2759 | 78.40% | 0.60% | 0.58% | 20.37% | NA |
| All Japonica | 1512 | 26.60% | 0.30% | 0.60% | 72.55% | NA |
| Aus | 269 | 49.10% | 1.90% | 1.86% | 47.21% | NA |
| Indica I | 595 | 62.50% | 0.50% | 1.01% | 35.97% | NA |
| Indica II | 465 | 78.90% | 0.00% | 0.43% | 20.65% | NA |
| Indica III | 913 | 88.10% | 0.70% | 0.22% | 11.06% | NA |
| Indica Intermediate | 786 | 79.00% | 1.00% | 0.76% | 19.21% | NA |
| Temperate Japonica | 767 | 10.40% | 0.00% | 0.26% | 89.31% | NA |
| Tropical Japonica | 504 | 47.40% | 0.80% | 0.99% | 50.79% | NA |
| Japonica Intermediate | 241 | 34.40% | 0.00% | 0.83% | 64.73% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 1.11% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960445 | T -> C | LOC_Os12g34580.1 | missense_variant ; p.Met610Thr; MODERATE | nonsynonymous_codon ; M610T | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1220960445 | T -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |