| Variant ID: vg0226608561 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 26608561 |
| Reference Allele: A | Alternative Allele: ACGGAAT,ACGGAATTGGAAGTTGTTCGG,ACGGAATTGGAAGTTGT,ACGGAATTGGAAGTTG,ACGGAATTGGAAG,ACGGAATTGGAAGT |
| Primary Allele: A | Secondary Allele: ACGGAATTGGAAGTTGTTCG G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 250. )
AATCGCAGAAAGTGACCTTTTACATGTACCGTGTTTGACAAAAAGAAGGTAAACCGGAAAATACAAAGCCTGTGAACGTATCACACACGACGAATATCAA[A/ACGGAAT,ACGGAATTGGAAGTTGTTCGG,ACGGAATTGGAAGTTGT,ACGGAATTGGAAGTTG,ACGGAATTGGAAG,ACGGAATTGGAAGT]
TCAAGCAAACGTACGATGCATGCAAACTGACACGGATACTTCAATTAATTCGGTTCATCCACTTTTAAGCGTAGTCCTGGTCGGCAACGGGCTGGTATGA
TCATACCAGCCCGTTGCCGACCAGGACTACGCTTAAAAGTGGATGAACCGAATTAATTGAAGTATCCGTGTCAGTTTGCATGCATCGTACGTTTGCTTGA[T/ATTCCGT,CCGAACAACTTCCAATTCCGT,ACAACTTCCAATTCCGT,CAACTTCCAATTCCGT,CTTCCAATTCCGT,ACTTCCAATTCCGT]
TTGATATTCGTCGTGTGTGATACGTTCACAGGCTTTGTATTTTCCGGTTTACCTTCTTTTTGTCAAACACGGTACATGTAAAAGGTCACTTTCTGCGATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ACGGAATTGGAAGTTGTTCG G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.10% | 0.02% | 0.00% | ACGGAAT: 0.15%; ACGGAATTGGAAGTTGT: 0.08%; ACGGAATTGGAAGT: 0.08%; ACGGAATTGGAAG: 0.04%; ACGGAATTGGAAGTTG: 0.02% |
| All Indica | 2759 | 99.10% | 0.30% | 0.04% | 0.00% | ACGGAAT: 0.25%; ACGGAATTGGAAGTTGT: 0.14%; ACGGAATTGGAAGT: 0.14%; ACGGAATTGGAAG: 0.07%; ACGGAATTGGAAGTTG: 0.04% |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.20% | 0.17% | 0.00% | ACGGAAT: 0.50% |
| Indica II | 465 | 99.60% | 0.20% | 0.00% | 0.00% | ACGGAAT: 0.22% |
| Indica III | 913 | 98.90% | 0.00% | 0.00% | 0.00% | ACGGAATTGGAAGT: 0.33%; ACGGAAT: 0.22%; ACGGAATTGGAAGTTGT: 0.22%; ACGGAATTGGAAG: 0.22%; ACGGAATTGGAAGTTG: 0.11% |
| Indica Intermediate | 786 | 98.90% | 0.60% | 0.00% | 0.00% | ACGGAATTGGAAGTTGT: 0.25%; ACGGAAT: 0.13%; ACGGAATTGGAAGT: 0.13% |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0226608561 | A -> ACGGAATTGGAAGTTG | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0226608561 | A -> ACGGAATTGGAAG | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0226608561 | A -> ACGGAAT | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0226608561 | A -> ACGGAATTGGAAGTTGTTCGG | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0226608561 | A -> ACGGAATTGGAAGTTGT | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0226608561 | A -> ACGGAATTGGAAGT | LOC_Os02g44080.1 | 3_prime_UTR_variant ; 64.0bp to feature; MODIFIER | N | Average:68.411; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |