| Variant ID: vg0430653750 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30653750 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, A: 0.16, others allele: 0.00, population size: 90. )
AGTAGTCGCCGAAGAGTTCACTAGTGAATTGGGTGCCATTATCCGTAATGATACGGTTAGGCACTCCAAAACGGGCCGTGATGCCCTTAATGAATTTAAG[T/A]
GCAGAGTGCTTATCGATCTTGACGACCGGATAAGCCTCGGGCCACTTAGTGAACTTGTCGATCGCGACATACAGATACTCAAACCCGCCCGGGGCCCGCT
AGCGGGCCCCGGGCGGGTTTGAGTATCTGTATGTCGCGATCGACAAGTTCACTAAGTGGCCCGAGGCTTATCCGGTCGTCAAGATCGATAAGCACTCTGC[A/T]
CTTAAATTCATTAAGGGCATCACGGCCCGTTTTGGAGTGCCTAACCGTATCATTACGGATAATGGCACCCAATTCACTAGTGAACTCTTCGGCGACTACT
| 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 | 41.60% | 9.00% | 29.88% | 19.53% | NA |
| All Indica | 2759 | 42.90% | 12.20% | 43.06% | 1.85% | NA |
| All Japonica | 1512 | 39.60% | 3.10% | 6.81% | 50.46% | NA |
| Aus | 269 | 38.70% | 7.10% | 26.77% | 27.51% | NA |
| Indica I | 595 | 47.70% | 3.50% | 47.39% | 1.34% | NA |
| Indica II | 465 | 38.50% | 18.50% | 40.86% | 2.15% | NA |
| Indica III | 913 | 42.10% | 16.90% | 40.42% | 0.66% | NA |
| Indica Intermediate | 786 | 42.70% | 9.70% | 44.15% | 3.44% | NA |
| Temperate Japonica | 767 | 63.20% | 1.20% | 0.39% | 35.20% | NA |
| Tropical Japonica | 504 | 11.10% | 6.50% | 12.70% | 69.64% | NA |
| Japonica Intermediate | 241 | 24.10% | 2.10% | 14.94% | 58.92% | NA |
| VI/Aromatic | 96 | 44.80% | 15.60% | 18.75% | 20.83% | NA |
| Intermediate | 90 | 38.90% | 10.00% | 34.44% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430653750 | T -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0430653750 | T -> A | LOC_Os04g51730.1 | synonymous_variant ; p.Ala204Ala; LOW | synonymous_codon | Average:11.428; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |