| Variant ID: vg0323735375 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 23735375 |
| Reference Allele: CAT | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: CAT |
Inferred Ancestral Allele: Not determined.
GTACCTTTATAGTTGCACCCGAAAATTTTAATAAAATTTCTACACGTGCACTTACATTATTATCGAATTGTACGGGTGTAGTTTAGTGGTCACTGGTGAT[CAT/C]
ATCACTGCATGCATACACTACAAATGCACACGTACAAATGAATGAATTGATCAATCGTTCTTACACATGAACGCAATGTTGATGGATGTGATATGCAGGC
GCCTGCATATCACATCCATCAACATTGCGTTCATGTGTAAGAACGATTGATCAATTCATTCATTTGTACGTGTGCATTTGTAGTGTATGCATGCAGTGAT[ATG/G]
ATCACCAGTGACCACTAAACTACACCCGTACAATTCGATAATAATGTAAGTGCACGTGTAGAAATTTTATTAAAATTTTCGGGTGCAACTATAAAGGTAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.10% | 35.80% | 4.36% | 16.74% | NA |
| All Indica | 2759 | 61.50% | 3.20% | 7.18% | 28.09% | NA |
| All Japonica | 1512 | 1.80% | 97.90% | 0.00% | 0.26% | NA |
| Aus | 269 | 94.10% | 5.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 50.30% | 1.00% | 6.05% | 42.69% | NA |
| Indica II | 465 | 88.80% | 1.50% | 3.23% | 6.45% | NA |
| Indica III | 913 | 52.10% | 3.70% | 9.31% | 34.83% | NA |
| Indica Intermediate | 786 | 64.90% | 5.20% | 7.89% | 22.01% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.00% | 95.40% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 1.20% | 98.30% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 27.10% | 71.90% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 34.40% | 45.60% | 7.78% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0323735375 | CAT -> C | LOC_Os03g42650.1 | upstream_gene_variant ; 3509.0bp to feature; MODIFIER | silent_mutation | Average:74.264; most accessible tissue: Minghui63 flower, score: 85.0 | N | N | N | N |
| vg0323735375 | CAT -> C | LOC_Os03g42650.2 | upstream_gene_variant ; 3509.0bp to feature; MODIFIER | silent_mutation | Average:74.264; most accessible tissue: Minghui63 flower, score: 85.0 | N | N | N | N |
| vg0323735375 | CAT -> C | LOC_Os03g42630.1 | intron_variant ; MODIFIER | silent_mutation | Average:74.264; most accessible tissue: Minghui63 flower, score: 85.0 | N | N | N | N |
| vg0323735375 | CAT -> DEL | N | N | silent_mutation | Average:74.264; most accessible tissue: Minghui63 flower, score: 85.0 | N | N | N | N |