| Variant ID: vg1222999904 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999904 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AACATAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAA[C/T]
TTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATAT
ATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAA[G/A]
TTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTATGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.00% | 0.40% | 10.56% | 44.03% | NA |
| All Indica | 2759 | 49.20% | 0.50% | 6.45% | 43.78% | NA |
| All Japonica | 1512 | 41.10% | 0.00% | 9.85% | 49.07% | NA |
| Aus | 269 | 26.00% | 1.90% | 54.65% | 17.47% | NA |
| Indica I | 595 | 31.60% | 0.00% | 12.10% | 56.30% | NA |
| Indica II | 465 | 51.40% | 1.30% | 2.58% | 44.73% | NA |
| Indica III | 913 | 59.60% | 0.40% | 5.04% | 34.94% | NA |
| Indica Intermediate | 786 | 49.20% | 0.60% | 6.11% | 44.02% | NA |
| Temperate Japonica | 767 | 28.30% | 0.00% | 11.34% | 60.37% | NA |
| Tropical Japonica | 504 | 56.90% | 0.00% | 8.93% | 34.13% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 7.05% | 44.40% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 13.54% | 48.96% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 13.33% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999904 | C -> DEL | N | N | silent_mutation | Average:29.622; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999904 | C -> T | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 354.0bp to feature; MODIFIER | silent_mutation | Average:29.622; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999904 | C -> T | LOC_Os12g37470.1 | upstream_gene_variant ; 1380.0bp to feature; MODIFIER | silent_mutation | Average:29.622; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999904 | C -> T | LOC_Os12g37490.1 | downstream_gene_variant ; 2307.0bp to feature; MODIFIER | silent_mutation | Average:29.622; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |