| Variant ID: vg0307992391 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 7992391 |
| Reference Allele: TAAAA | Alternative Allele: TAA,TTAAAAA,AAAAA,TA,T,TTAAAAAA |
| Primary Allele: TAAAA | Secondary Allele: TAA |
Inferred Ancestral Allele: Not determined.
ACACCCATTCTGGGAGATTTTCTCCACATATTTTCTTCACGTCTTCGCGGTCGAGAGATGCAAGTGCATTGACATCTGCAGCCTGATACAGAATTTTTTT[TAAAA/TAA,TTAAAAA,AAAAA,TA,T,TTAAAAAA]
AAAAAAAAGTTAGCCACAAACCAATCTGTTTGCACCAAATAACGTCTCACTTATCATCACCATTTTATATCAACAGTATACAAATTCAACTAAACATAGA
TCTATGTTTAGTTGAATTTGTATACTGTTGATATAAAATGGTGATGATAAGTGAGACGTTATTTGGTGCAAACAGATTGGTTTGTGGCTAACTTTTTTTT[TTTTA/TTA,TTTTTAA,TTTTT,TA,A,TTTTTTAA]
AAAAAAATTCTGTATCAGGCTGCAGATGTCAATGCACTTGCATCTCTCGACCGCGAAGACGTGAAGAAAATATGTGGAGAAAATCTCCCAGAATGGGTGT
| Populations | Population Size | Frequency of TAAAA(primary allele) | Frequency of TAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 26.60% | 6.41% | 0.00% | TTAAAAA: 8.17%; AAAAA: 7.49%; TA: 7.45%; T: 0.36%; TTAAAAAA: 0.02% |
| All Indica | 2759 | 23.00% | 43.30% | 7.87% | 0.00% | TTAAAAA: 13.37%; TA: 12.25%; AAAAA: 0.14%; T: 0.07%; TTAAAAAA: 0.04% |
| All Japonica | 1512 | 69.70% | 2.90% | 4.76% | 0.00% | AAAAA: 21.23%; T: 0.99%; TA: 0.26%; TTAAAAA: 0.13% |
| Aus | 269 | 95.90% | 2.60% | 0.37% | 0.00% | TTAAAAA: 1.12% |
| Indica I | 595 | 27.20% | 50.80% | 15.80% | 0.00% | TA: 6.05%; TTAAAAA: 0.17% |
| Indica II | 465 | 14.20% | 26.90% | 11.18% | 0.00% | TA: 45.16%; TTAAAAA: 2.15%; AAAAA: 0.22%; TTAAAAAA: 0.22% |
| Indica III | 913 | 19.30% | 49.40% | 1.31% | 0.00% | TTAAAAA: 28.15%; TA: 1.53%; AAAAA: 0.22%; T: 0.11% |
| Indica Intermediate | 786 | 29.30% | 40.20% | 7.51% | 0.00% | TTAAAAA: 12.85%; TA: 9.92%; AAAAA: 0.13%; T: 0.13% |
| Temperate Japonica | 767 | 66.60% | 0.80% | 6.00% | 0.00% | AAAAA: 24.25%; T: 1.69%; TA: 0.39%; TTAAAAA: 0.26% |
| Tropical Japonica | 504 | 69.00% | 7.30% | 3.17% | 0.00% | AAAAA: 20.44% |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 4.15% | 0.00% | AAAAA: 13.28%; T: 0.83%; TA: 0.41% |
| VI/Aromatic | 96 | 66.70% | 3.10% | 3.12% | 0.00% | AAAAA: 23.96%; TTAAAAA: 3.12% |
| Intermediate | 90 | 48.90% | 12.20% | 11.11% | 0.00% | TA: 11.11%; TTAAAAA: 10.00%; AAAAA: 6.67% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0307992391 | TAAAA -> TTAAAAAA | LOC_Os03g14690.1 | downstream_gene_variant ; 2955.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TTAAAAAA | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> T | LOC_Os03g14690.1 | downstream_gene_variant ; 2955.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> T | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TA | LOC_Os03g14690.1 | downstream_gene_variant ; 2956.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TA | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TAA | LOC_Os03g14690.1 | downstream_gene_variant ; 2957.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TAA | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> AAAAA | LOC_Os03g14690.1 | downstream_gene_variant ; 2954.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> AAAAA | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TTAAAAA | LOC_Os03g14690.1 | downstream_gene_variant ; 2955.0bp to feature; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| vg0307992391 | TAAAA -> TTAAAAA | LOC_Os03g14700.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.79; most accessible tissue: Callus, score: 51.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0307992391 | 5.01E-07 | NA | mr1300 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0307992391 | NA | 1.62E-06 | mr1305 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0307992391 | 7.36E-07 | NA | mr1310 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0307992391 | NA | 3.94E-07 | mr1585 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0307992391 | 1.21E-07 | NA | mr1926 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0307992391 | 5.75E-08 | NA | mr1310_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |