| Variant ID: vg0918111800 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 18111800 |
| Reference Allele: CTTTT | Alternative Allele: C,CT,CTTT,CTT,CTTTTT |
| Primary Allele: CTTTT | Secondary Allele: CTTT |
Inferred Ancestral Allele: Not determined.
TTCGCGATCTCCCTCTGTTACTATGCTCCTTGTTTTACTGCAATGCGTGCTCTGTGTTTGCGTAATTGCTTGTATGAACGCTGCCTCACTCACGGTTAGG[CTTTT/C,CT,CTTT,CTT,CTTTTT]
TTTTTTTTTTGCCGGTAATATTACACAGAGTACGAACTCTGTAAACGCGCTGATGTGTAGTCGCTATCTTTTATACTACTGTTGTGGGTGTGGCACAATG
CATTGTGCCACACCCACAACAGTAGTATAAAAGATAGCGACTACACATCAGCGCGTTTACAGAGTTCGTACTCTGTGTAATATTACCGGCAAAAAAAAAA[AAAAG/G,AG,AAAG,AAG,AAAAAG]
CCTAACCGTGAGTGAGGCAGCGTTCATACAAGCAATTACGCAAACACAGAGCACGCATTGCAGTAAAACAAGGAGCATAGTAACAGAGGGAGATCGCGAA
| Populations | Population Size | Frequency of CTTTT(primary allele) | Frequency of CTTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.70% | 36.70% | 11.15% | 0.00% | CT: 10.07%; CTT: 1.21%; CTTTTT: 0.23% |
| All Indica | 2759 | 14.60% | 53.60% | 14.06% | 0.00% | CT: 17.04%; CTT: 0.69% |
| All Japonica | 1512 | 90.80% | 4.60% | 3.77% | 0.00% | CTTTTT: 0.73%; CTT: 0.07% |
| Aus | 269 | 19.70% | 45.70% | 20.82% | 0.00% | CTT: 13.38%; CT: 0.37% |
| Indica I | 595 | 14.10% | 30.40% | 10.08% | 0.00% | CT: 45.38% |
| Indica II | 465 | 14.00% | 57.00% | 24.09% | 0.00% | CT: 4.73%; CTT: 0.22% |
| Indica III | 913 | 15.30% | 71.60% | 10.62% | 0.00% | CTT: 1.20%; CT: 1.20% |
| Indica Intermediate | 786 | 14.40% | 48.30% | 15.14% | 0.00% | CT: 21.25%; CTT: 0.89% |
| Temperate Japonica | 767 | 87.00% | 7.00% | 5.61% | 0.00% | CTTTTT: 0.39% |
| Tropical Japonica | 504 | 96.20% | 2.60% | 0.79% | 0.00% | CTTTTT: 0.40% |
| Japonica Intermediate | 241 | 91.70% | 1.20% | 4.15% | 0.00% | CTTTTT: 2.49%; CTT: 0.41% |
| VI/Aromatic | 96 | 40.60% | 42.70% | 15.62% | 0.00% | CTT: 1.04% |
| Intermediate | 90 | 61.10% | 21.10% | 12.22% | 0.00% | CT: 5.56% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0918111800 | CTTTT -> CTT | LOC_Os09g29790.1 | upstream_gene_variant ; 2490.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTT | LOC_Os09g29810.1 | upstream_gene_variant ; 3322.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTT | LOC_Os09g29790.1 | upstream_gene_variant ; 2491.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTT | LOC_Os09g29810.1 | upstream_gene_variant ; 3321.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTTTT | LOC_Os09g29790.1 | upstream_gene_variant ; 2492.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTTTT | LOC_Os09g29810.1 | upstream_gene_variant ; 3320.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CTTTTT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> C | LOC_Os09g29790.1 | upstream_gene_variant ; 2488.0bp to feature; MODIFIER | N | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> C | LOC_Os09g29810.1 | upstream_gene_variant ; 3324.0bp to feature; MODIFIER | N | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> C | LOC_Os09g29800.1 | intron_variant ; MODIFIER | N | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CT | LOC_Os09g29790.1 | upstream_gene_variant ; 2489.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CT | LOC_Os09g29810.1 | upstream_gene_variant ; 3323.0bp to feature; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |
| vg0918111800 | CTTTT -> CT | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:80.205; most accessible tissue: Callus, score: 84.784 | N | N | N | N |