| Variant ID: vg0222979993 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 22979993 |
| Reference Allele: ATT | Alternative Allele: ATTT,AT,A,TTT |
| Primary Allele: ATT | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
CCAAAAATAATGGATGACGGGTAGAACGCAATGCTGGTTAATTAAAATTGTCACTGAAAGCAATCCACTTATGAGTTAGGTTTATGAGAATTGTTTTTGC[ATT/ATTT,AT,A,TTT]
TTTTTTTTAAGATCACGCATGTTTATTTTTGATATCATGATTATTGAACACGAATGAATTATGAGCATAGAGGAGTCAAATATGGTATAAAAAAGAAATC
GATTTCTTTTTTATACCATATTTGACTCCTCTATGCTCATAATTCATTCGTGTTCAATAATCATGATATCAAAAATAAACATGCGTGATCTTAAAAAAAA[AAT/AAAT,AT,T,AAA]
GCAAAAACAATTCTCATAAACCTAACTCATAAGTGGATTGCTTTCAGTGACAATTTTAATTAACCAGCATTGCGTTCTACCCGTCATCCATTATTTTTGG
| Populations | Population Size | Frequency of ATT(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.30% | 7.70% | 2.43% | 0.53% | A: 3.91%; ATTT: 0.08%; TTT: 0.02% |
| All Indica | 2759 | 81.20% | 12.60% | 3.55% | 0.87% | A: 1.56%; ATTT: 0.11%; TTT: 0.04% |
| All Japonica | 1512 | 98.50% | 0.50% | 0.79% | 0.07% | A: 0.07% |
| Aus | 269 | 48.00% | 0.70% | 0.37% | 0.00% | A: 50.93% |
| Indica I | 595 | 61.30% | 25.70% | 11.26% | 1.51% | A: 0.17% |
| Indica II | 465 | 80.60% | 14.60% | 1.72% | 1.51% | A: 1.51% |
| Indica III | 913 | 93.60% | 3.70% | 0.11% | 0.44% | A: 1.75%; ATTT: 0.33% |
| Indica Intermediate | 786 | 82.20% | 12.00% | 2.80% | 0.51% | A: 2.42%; TTT: 0.13% |
| Temperate Japonica | 767 | 97.90% | 0.80% | 1.30% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.00% | A: 0.41% |
| VI/Aromatic | 96 | 94.80% | 2.10% | 1.04% | 0.00% | ATTT: 1.04%; A: 1.04% |
| Intermediate | 90 | 88.90% | 4.40% | 3.33% | 0.00% | A: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222979993 | ATT -> A | LOC_Os02g38029.1 | upstream_gene_variant ; 3358.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38020.1 | downstream_gene_variant ; 4698.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.1 | downstream_gene_variant ; 1852.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38020.2 | downstream_gene_variant ; 4698.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.4 | downstream_gene_variant ; 1839.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.3 | downstream_gene_variant ; 1839.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.5 | downstream_gene_variant ; 1839.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.6 | downstream_gene_variant ; 1839.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38050.2 | downstream_gene_variant ; 1852.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> A | LOC_Os02g38040.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> DEL | N | N | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38029.1 | upstream_gene_variant ; 3360.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38020.1 | downstream_gene_variant ; 4700.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.1 | downstream_gene_variant ; 1850.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38020.2 | downstream_gene_variant ; 4700.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.4 | downstream_gene_variant ; 1837.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.3 | downstream_gene_variant ; 1837.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.5 | downstream_gene_variant ; 1837.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.6 | downstream_gene_variant ; 1837.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38050.2 | downstream_gene_variant ; 1850.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> ATTT | LOC_Os02g38040.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38029.1 | upstream_gene_variant ; 3357.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38020.1 | downstream_gene_variant ; 4697.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.1 | downstream_gene_variant ; 1853.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38020.2 | downstream_gene_variant ; 4697.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.4 | downstream_gene_variant ; 1840.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.3 | downstream_gene_variant ; 1840.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.5 | downstream_gene_variant ; 1840.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.6 | downstream_gene_variant ; 1840.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38050.2 | downstream_gene_variant ; 1853.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> TTT | LOC_Os02g38040.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38029.1 | upstream_gene_variant ; 3359.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38020.1 | downstream_gene_variant ; 4699.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.1 | downstream_gene_variant ; 1851.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38020.2 | downstream_gene_variant ; 4699.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.4 | downstream_gene_variant ; 1838.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.3 | downstream_gene_variant ; 1838.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.5 | downstream_gene_variant ; 1838.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.6 | downstream_gene_variant ; 1838.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38050.2 | downstream_gene_variant ; 1851.0bp to feature; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |
| vg0222979993 | ATT -> AT | LOC_Os02g38040.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.89; most accessible tissue: Callus, score: 82.461 | N | N | N | N |