| Variant ID: vg1222999909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22999909 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTTCATATTATAAAACTTTG[T/C]
AACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATATATA
TATATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTT[A/G]
CAAAGTTTTATAATATGAAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATT
| 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 | 39.10% | 4.50% | 13.73% | 42.62% | NA |
| All Indica | 2759 | 47.60% | 5.90% | 15.59% | 30.92% | NA |
| All Japonica | 1512 | 20.60% | 2.50% | 11.57% | 65.34% | NA |
| Aus | 269 | 63.60% | 3.70% | 6.69% | 26.02% | NA |
| Indica I | 595 | 19.50% | 7.10% | 21.85% | 51.60% | NA |
| Indica II | 465 | 55.50% | 0.40% | 9.25% | 34.84% | NA |
| Indica III | 913 | 65.10% | 4.40% | 15.01% | 15.55% | NA |
| Indica Intermediate | 786 | 44.00% | 9.90% | 15.27% | 30.79% | NA |
| Temperate Japonica | 767 | 14.90% | 2.50% | 8.87% | 73.79% | NA |
| Tropical Japonica | 504 | 28.80% | 0.60% | 15.28% | 55.36% | NA |
| Japonica Intermediate | 241 | 21.60% | 6.60% | 12.45% | 59.34% | NA |
| VI/Aromatic | 96 | 25.00% | 2.10% | 9.38% | 63.54% | NA |
| Intermediate | 90 | 31.10% | 3.30% | 18.89% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999909 | T -> C | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 349.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999909 | T -> C | LOC_Os12g37470.1 | upstream_gene_variant ; 1385.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999909 | T -> C | LOC_Os12g37490.1 | downstream_gene_variant ; 2302.0bp to feature; MODIFIER | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |
| vg1222999909 | T -> DEL | N | N | silent_mutation | Average:29.24; most accessible tissue: Zhenshan97 flower, score: 44.193 | N | N | N | N |