| Variant ID: vg0825763600 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 25763600 |
| Reference Allele: GT | Alternative Allele: G,GTT |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CATCATCAGTCCAATCCGTGCGTGCATATAGCTCAATCACTATCACAGTAATCATTACTTAGTACATGTTGTTTTGTAATCTTTGCTAGCGAAAGCTAGT[GT/G,GTT]
TTTTTTTTTATGTGCACAACTCGGTGTGCCGCCATACATGCATGTGTGATCGACGTATCAGTCTGTACTCTCCCTTTTTTATCTTGCTAGCGAAAGCTAG
CTAGCTTTCGCTAGCAAGATAAAAAAGGGAGAGTACAGACTGATACGTCGATCACACATGCATGTATGGCGGCACACCGAGTTGTGCACATAAAAAAAAA[AC/C,AAC]
ACTAGCTTTCGCTAGCAAAGATTACAAAACAACATGTACTAAGTAATGATTACTGTGATAGTGATTGAGCTATATGCACGCACGGATTGGACTGATGATG
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.50% | 0.32% | 0.00% | GTT: 0.08% |
| All Indica | 2759 | 99.00% | 0.70% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.20% | 0.40% | 0.00% | GTT: 0.26% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.10% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.13% | 0.00% | GTT: 0.13% |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.40% | 0.00% | GTT: 0.60% |
| Japonica Intermediate | 241 | 97.90% | 0.80% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825763600 | GT -> G | LOC_Os08g40690.1 | 3_prime_UTR_variant ; 165.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> G | LOC_Os08g40680.1 | upstream_gene_variant ; 3652.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> G | LOC_Os08g40700.1 | upstream_gene_variant ; 1372.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> G | LOC_Os08g40710.1 | downstream_gene_variant ; 3948.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> GTT | LOC_Os08g40690.1 | 3_prime_UTR_variant ; 166.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> GTT | LOC_Os08g40680.1 | upstream_gene_variant ; 3653.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> GTT | LOC_Os08g40700.1 | upstream_gene_variant ; 1371.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |
| vg0825763600 | GT -> GTT | LOC_Os08g40710.1 | downstream_gene_variant ; 3947.0bp to feature; MODIFIER | silent_mutation | Average:67.329; most accessible tissue: Minghui63 panicle, score: 89.949 | N | N | N | N |