| Variant ID: vg0218608139 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 18608139 |
| Reference Allele: T | Alternative Allele: TG,TTG,G,TTTG,TTTTTTTTG,TTTTG |
| Primary Allele: T | Secondary Allele: TG |
Inferred Ancestral Allele: Not determined.
GGCTGGCCTATGGCGAGAGCCGAGAGGGGGCCTTTTCTTCAGGTGTTGTGGGTTCACACGAGAGAGATATATATAGAAACATGCCGTCATGTTTTTTTTT[T/TG,TTG,G,TTTG,TTTTTTTTG,TTTTG]
AACGACTCGCACTAGACGGTGTGAAATTCTATTGATAGAGCAGAAAAAAATTACAAGATTACAACCTTGCAAGGTCGTAACCAGAAAAAAAGAAAATTAT
ATAATTTTCTTTTTTTCTGGTTACGACCTTGCAAGGTTGTAATCTTGTAATTTTTTTCTGCTCTATCAATAGAATTTCACACCGTCTAGTGCGAGTCGTT[A/CA,CAA,C,CAAA,CAAAAAAAA,CAAAA]
AAAAAAAAACATGACGGCATGTTTCTATATATATCTCTCTCGTGTGAACCCACAACACCTGAAGAAAAGGCCCCCTCTCGGCTCTCGCCATAGGCCAGCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.90% | 14.00% | 0.72% | 0.00% | TTG: 8.74%; G: 4.42%; TTTG: 0.17%; TTTTTTTTG: 0.02%; TTTTG: 0.02% |
| All Indica | 2759 | 76.80% | 12.30% | 0.51% | 0.00% | TTG: 7.18%; G: 3.19%; TTTG: 0.04%; TTTTG: 0.04% |
| All Japonica | 1512 | 71.80% | 18.80% | 0.53% | 0.00% | G: 7.47%; TTG: 1.39% |
| Aus | 269 | 40.90% | 2.20% | 2.23% | 0.00% | TTG: 51.67%; TTTG: 2.60%; TTTTTTTTG: 0.37% |
| Indica I | 595 | 82.40% | 0.00% | 0.84% | 0.00% | TTG: 16.64%; G: 0.17% |
| Indica II | 465 | 84.10% | 5.20% | 0.86% | 0.00% | G: 6.02%; TTG: 3.87% |
| Indica III | 913 | 65.70% | 26.80% | 0.22% | 0.00% | G: 3.61%; TTG: 3.40%; TTTTG: 0.11%; TTTG: 0.11% |
| Indica Intermediate | 786 | 81.00% | 8.90% | 0.38% | 0.00% | TTG: 6.36%; G: 3.31% |
| Temperate Japonica | 767 | 99.10% | 0.70% | 0.13% | 0.00% | G: 0.13% |
| Tropical Japonica | 504 | 34.90% | 41.70% | 0.60% | 0.00% | G: 21.43%; TTG: 1.39% |
| Japonica Intermediate | 241 | 61.80% | 29.00% | 1.66% | 0.00% | TTG: 5.81%; G: 1.66% |
| VI/Aromatic | 96 | 27.10% | 22.90% | 2.08% | 0.00% | TTG: 44.79%; G: 3.12% |
| Intermediate | 90 | 65.60% | 11.10% | 4.44% | 0.00% | TTG: 13.33%; G: 5.56% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0218608139 | T -> TTTTTTTTG | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0218608139 | T -> TTG | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0218608139 | T -> TTTTG | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0218608139 | T -> TG | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0218608139 | T -> G | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| vg0218608139 | T -> TTTG | LOC_Os02g31120.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.152; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0218608139 | 2.77E-07 | 2.59E-09 | mr1076 | Jap_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 |
| vg0218608139 | NA | 2.22E-08 | mr1082 | 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 |
| vg0218608139 | 5.21E-08 | 1.39E-11 | mr1083 | Jap_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 |
| vg0218608139 | 4.26E-07 | 5.65E-10 | mr1226 | 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 |
| vg0218608139 | 6.92E-06 | 8.07E-08 | mr1227 | 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 |
| vg0218608139 | 1.56E-07 | 1.56E-07 | mr1076_2 | 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 |
| vg0218608139 | 8.72E-06 | 1.72E-10 | mr1082_2 | 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 |
| vg0218608139 | NA | 2.87E-08 | mr1083_2 | 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 |
| vg0218608139 | NA | 1.29E-06 | mr1104_2 | 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 |
| vg0218608139 | NA | 9.25E-07 | mr1107_2 | 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 |
| vg0218608139 | NA | 3.03E-08 | mr1226_2 | 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 |