| Variant ID: vg1222999884 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 22999884 |
| Reference Allele: C | Alternative Allele: CTAATTACT |
| Primary Allele: C | Secondary Allele: CTAATTACT |
Inferred Ancestral Allele: Not determined.
CAACAATACATGAACACACAAACATAATCAAGACGCTTCCACTAACATTTGTGAGGTGTGAAGGATGGATTTGATACACGGTCATCATAATAATTACTTC[C/CTAATTACT]
TCCATTTCATATTATAAAACTTTGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACAC
GTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACAAAGTTTTATAATATGAAATGGA[G/AGTAATTAG]
GAAGTAATTATTATGATGACCGTGTATCAAATCCATCCTTCACACCTCACAAATGTTAGTGGAAGCGTCTTGATTATGTTTGTGTGTTCATGTATTGTTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTAATTACT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 0.20% | 8.84% | 47.48% | NA |
| All Indica | 2759 | 48.20% | 0.10% | 9.97% | 41.72% | NA |
| All Japonica | 1512 | 38.90% | 0.00% | 3.37% | 57.74% | NA |
| Aus | 269 | 24.50% | 2.20% | 27.14% | 46.10% | NA |
| Indica I | 595 | 28.10% | 0.00% | 6.22% | 65.71% | NA |
| Indica II | 465 | 50.50% | 0.00% | 8.60% | 40.86% | NA |
| Indica III | 913 | 60.00% | 0.20% | 12.71% | 27.05% | NA |
| Indica Intermediate | 786 | 48.50% | 0.00% | 10.43% | 41.09% | NA |
| Temperate Japonica | 767 | 26.90% | 0.00% | 2.35% | 70.80% | NA |
| Tropical Japonica | 504 | 53.60% | 0.00% | 4.37% | 42.06% | NA |
| Japonica Intermediate | 241 | 46.50% | 0.00% | 4.56% | 48.96% | NA |
| VI/Aromatic | 96 | 31.20% | 0.00% | 8.33% | 60.42% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 12.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222999884 | C -> DEL | N | N | silent_mutation | Average:28.602; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999884 | C -> CTAATTACT | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 373.0bp to feature; MODIFIER | silent_mutation | Average:28.602; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999884 | C -> CTAATTACT | LOC_Os12g37470.1 | upstream_gene_variant ; 1361.0bp to feature; MODIFIER | silent_mutation | Average:28.602; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
| vg1222999884 | C -> CTAATTACT | LOC_Os12g37490.1 | downstream_gene_variant ; 2326.0bp to feature; MODIFIER | silent_mutation | Average:28.602; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |