| Variant ID: vg1222999892 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22999892 |
| Reference Allele: CAT | Alternative Allele: C,TAT |
| Primary Allele: CAT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATGAACACACAAACATAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTCCTCCATTT[CAT/C,TAT]
ATTATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATAT
ATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTATAAT[ATG/G,ATA]
AAATGGAGGAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTATGTTTGTGTGTTCATG
| Populations | Population Size | Frequency of CAT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.80% | 0.40% | 11.66% | 44.05% | TAT: 0.06% |
| All Indica | 2759 | 47.70% | 0.50% | 8.01% | 43.71% | TAT: 0.04% |
| All Japonica | 1512 | 40.70% | 0.00% | 9.99% | 49.27% | NA |
| Aus | 269 | 26.00% | 2.20% | 54.28% | 17.47% | NA |
| Indica I | 595 | 25.70% | 0.00% | 17.82% | 56.30% | TAT: 0.17% |
| Indica II | 465 | 51.00% | 1.30% | 2.80% | 44.95% | NA |
| Indica III | 913 | 59.50% | 0.40% | 5.26% | 34.83% | NA |
| Indica Intermediate | 786 | 48.70% | 0.60% | 6.87% | 43.77% | NA |
| Temperate Japonica | 767 | 28.20% | 0.00% | 11.34% | 60.50% | NA |
| Tropical Japonica | 504 | 56.70% | 0.00% | 8.73% | 34.52% | NA |
| Japonica Intermediate | 241 | 47.30% | 0.00% | 8.30% | 44.40% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 20.83% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 14.44% | 41.11% | TAT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999892 | CAT -> C | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 364.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> C | LOC_Os12g37470.1 | upstream_gene_variant ; 1369.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> C | LOC_Os12g37490.1 | downstream_gene_variant ; 2318.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> DEL | N | N | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> TAT | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 366.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> TAT | LOC_Os12g37470.1 | upstream_gene_variant ; 1368.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999892 | CAT -> TAT | LOC_Os12g37490.1 | downstream_gene_variant ; 2319.0bp to feature; MODIFIER | silent_mutation | Average:29.34; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |