| Variant ID: vg1222999998 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999998 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATA[C/T]
ATATATATATATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGTTTAGATTTATTAACATCTATATAA
TTATATAGATGTTAATAAATCTAAACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATATATATATAT[G/A]
TATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTAT
| 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 | 0.50% | 0.20% | 9.42% | 89.89% | NA |
| All Indica | 2759 | 0.70% | 0.10% | 5.29% | 93.91% | NA |
| All Japonica | 1512 | 0.10% | 0.50% | 15.61% | 83.86% | NA |
| Aus | 269 | 0.40% | 0.40% | 14.87% | 84.39% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.18% | 98.66% | NA |
| Indica II | 465 | 0.00% | 0.20% | 8.82% | 90.97% | NA |
| Indica III | 913 | 1.30% | 0.10% | 5.91% | 92.66% | NA |
| Indica Intermediate | 786 | 0.90% | 0.00% | 5.60% | 93.51% | NA |
| Temperate Japonica | 767 | 0.00% | 0.50% | 12.13% | 87.35% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 18.45% | 81.55% | NA |
| Japonica Intermediate | 241 | 0.40% | 1.20% | 20.75% | 77.59% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 9.38% | 89.58% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 15.56% | 84.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999998 | C -> DEL | N | N | silent_mutation | Average:42.015; most accessible tissue: Minghui63 root, score: 65.927 | N | N | N | N |
| vg1222999998 | C -> T | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 260.0bp to feature; MODIFIER | silent_mutation | Average:42.015; most accessible tissue: Minghui63 root, score: 65.927 | N | N | N | N |
| vg1222999998 | C -> T | LOC_Os12g37470.1 | upstream_gene_variant ; 1474.0bp to feature; MODIFIER | silent_mutation | Average:42.015; most accessible tissue: Minghui63 root, score: 65.927 | N | N | N | N |
| vg1222999998 | C -> T | LOC_Os12g37490.1 | downstream_gene_variant ; 2213.0bp to feature; MODIFIER | silent_mutation | Average:42.015; most accessible tissue: Minghui63 root, score: 65.927 | N | N | N | N |