| Variant ID: vg0604111550 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 4111550 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTCTGCAAGATACAAAAAAATGTATTAGGATAAATGCGAAGTAACATATATACATATATATATACATATATATACATATATATACATATATATACACATA[T/C]
ATATATACATATATATATATATATACATATATATATATATATATATATATATATATATATTGCATTTCACGTTAACGTTCGTCCTCGTTCGTTCGCTCGT
ACGAGCGAACGAACGAGGACGAACGTTAACGTGAAATGCAATATATATATATATATATATATATATATATATATGTATATATATATATATATGTATATAT[A/G]
TATGTGTATATATATGTATATATATGTATATATATGTATATATATATGTATATATGTTACTTCGCATTTATCCTAATACATTTTTTTGTATCTTGCAGAA
| 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 | 4.80% | 0.20% | 27.06% | 67.90% | NA |
| All Indica | 2759 | 4.60% | 0.40% | 27.26% | 67.74% | NA |
| All Japonica | 1512 | 6.10% | 0.00% | 28.31% | 65.61% | NA |
| Aus | 269 | 0.00% | 0.00% | 23.05% | 76.95% | NA |
| Indica I | 595 | 2.00% | 1.00% | 17.82% | 79.16% | NA |
| Indica II | 465 | 2.20% | 0.60% | 21.72% | 75.48% | NA |
| Indica III | 913 | 7.60% | 0.00% | 37.68% | 54.76% | NA |
| Indica Intermediate | 786 | 4.70% | 0.10% | 25.57% | 69.59% | NA |
| Temperate Japonica | 767 | 8.60% | 0.00% | 41.33% | 50.07% | NA |
| Tropical Japonica | 504 | 2.20% | 0.00% | 8.73% | 89.09% | NA |
| Japonica Intermediate | 241 | 6.20% | 0.00% | 27.80% | 65.98% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 14.58% | 81.25% | NA |
| Intermediate | 90 | 4.40% | 0.00% | 25.56% | 70.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0604111550 | T -> C | LOC_Os06g08420.1 | downstream_gene_variant ; 1872.0bp to feature; MODIFIER | silent_mutation | Average:13.294; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0604111550 | T -> C | LOC_Os06g08410.1 | intron_variant ; MODIFIER | silent_mutation | Average:13.294; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0604111550 | T -> DEL | N | N | silent_mutation | Average:13.294; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |