| Variant ID: vg0137237011 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 37237011 |
| Reference Allele: ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG | Alternative Allele: CTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG,TTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG,A |
| Primary Allele: CTAGAATGACTTACATTATG AAACGGATATTTGAGTATAT ATG | Secondary Allele: ATAGAATGACTTACATTATG AAACGGATATTTGAGTATAT ATG |
Inferred Ancestral Allele: Not determined.
GACTGTGCTGCGACGTATTTATAATACTTCCTCCGTTCCATAATGTACATTATGTTATTCTAGCATTTTCTATATCCATATAATATAGATGTGGAAAATG[ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG/CTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG,TTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG,A]
TAGCACAGTGATGTGTAGGAGCATGTGTTGATTGCTTTCGGTTACCGGTCAGACGTTTAGACCGTAGCTTACCATTGCCCCCAGTTTAATTTCATTCGTT
AACGAATGAAATTAAACTGGGGGCAATGGTAAGCTACGGTCTAAACGTCTGACCGGTAACCGAAAGCAATCAACACATGCTCCTACACATCACTGTGCTA[CATATATACTCAAATATCCGTTTCATAATGTAAGTCATTCTAT/CATATATACTCAAATATCCGTTTCATAATGTAAGTCATTCTAG,CATATATACTCAAATATCCGTTTCATAATGTAAGTCATTCTAA,T]
CATTTTCCACATCTATATTATATGGATATAGAAAATGCTAGAATAACATAATGTACATTATGGAACGGAGGAAGTATTATAAATACGTCGCAGCACAGTC
| Populations | Population Size | Frequency of CTAGAATGACTTACATTATG AAACGGATATTTGAGTATAT ATG(primary allele) | Frequency of ATAGAATGACTTACATTATG AAACGGATATTTGAGTATAT ATG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.30% | 35.30% | 0.04% | 0.25% | TTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG: 0.08%; A: 0.02% |
| All Indica | 2759 | 98.00% | 1.50% | 0.04% | 0.29% | TTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG: 0.14% |
| All Japonica | 1512 | 2.10% | 97.80% | 0.00% | 0.13% | A: 0.07% |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.17% | 0.34% | NA |
| Indica II | 465 | 98.70% | 0.90% | 0.00% | 0.43% | NA |
| Indica III | 913 | 98.70% | 0.70% | 0.00% | 0.22% | TTAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG: 0.44% |
| Indica Intermediate | 786 | 95.70% | 4.10% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 1.40% | 98.30% | 0.00% | 0.13% | A: 0.13% |
| Tropical Japonica | 504 | 3.00% | 96.80% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 96.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 57.80% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> CTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 186.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> CTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64110.1 | upstream_gene_variant ; 1890.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> CTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64120.1 | upstream_gene_variant ; 4144.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> CTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64090.1 | downstream_gene_variant ; 2636.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> TTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 186.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> TTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64110.1 | upstream_gene_variant ; 1890.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> TTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64120.1 | upstream_gene_variant ; 4144.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> TTAGAATGACTTACATTATGAAACGGATAT TTGAGTATATATG | LOC_Os01g64090.1 | downstream_gene_variant ; 2636.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> A | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 190.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> A | LOC_Os01g64110.1 | upstream_gene_variant ; 1889.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> A | LOC_Os01g64120.1 | upstream_gene_variant ; 4143.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> A | LOC_Os01g64090.1 | downstream_gene_variant ; 2637.0bp to feature; MODIFIER | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237011 | ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATG -> DEL | N | N | silent_mutation | Average:76.38; most accessible tissue: Callus, score: 91.532 | N | N | N | N |