| Variant ID: vg1013678979 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 13678979 |
| Reference Allele: CT | Alternative Allele: C,TT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele: Not determined.
CCAACCGACACTAAAGATCGTAACTAACACCAACCGGGACTAAAGTTCCCGGTGATCTTTAACCCCAGTTCATAACACCAACCGGGACTAAAGTCCCACC[CT/C,TT]
ATATATATATGTCTTCTTTCTCCTCCAGCCCGAGCAAGCTTCAAAATTTCTTCAAAAAAGAGGGGAGGTCATGCCAAAATTTCTAGTGAATTTATTTTGA
TCAAAATAAATTCACTAGAAATTTTGGCATGACCTCCCCTCTTTTTTGAAGAAATTTTGAAGCTTGCTCGGGCTGGAGGAGAAAGAAGACATATATATAT[AG/G,AA]
GGTGGGACTTTAGTCCCGGTTGGTGTTATGAACTGGGGTTAAAGATCACCGGGAACTTTAGTCCCGGTTGGTGTTAGTTACGATCTTTAGTGTCGGTTGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.60% | 20.80% | 0.44% | 1.65% | TT: 0.44% |
| All Indica | 2759 | 97.50% | 2.40% | 0.04% | 0.04% | NA |
| All Japonica | 1512 | 39.00% | 57.70% | 1.19% | 0.73% | TT: 1.39% |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.80% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 96.40% | 3.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 6.30% | 89.20% | 2.09% | 0.00% | TT: 2.48% |
| Tropical Japonica | 504 | 80.40% | 17.90% | 0.40% | 1.39% | NA |
| Japonica Intermediate | 241 | 56.40% | 41.10% | 0.00% | 1.66% | TT: 0.83% |
| VI/Aromatic | 96 | 32.30% | 2.10% | 1.04% | 64.58% | NA |
| Intermediate | 90 | 66.70% | 27.80% | 1.11% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1013678979 | CT -> C | LOC_Os10g26370.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.24; most accessible tissue: Callus, score: 45.722 | N | N | N | N |
| vg1013678979 | CT -> TT | LOC_Os10g26370.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.24; most accessible tissue: Callus, score: 45.722 | N | N | N | N |
| vg1013678979 | CT -> DEL | N | N | silent_mutation | Average:27.24; most accessible tissue: Callus, score: 45.722 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013678979 | NA | 5.00E-06 | mr1354 | 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 |
| vg1013678979 | NA | 4.88E-06 | mr1038_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 |
| vg1013678979 | NA | 4.27E-07 | mr1354_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 |
| vg1013678979 | 5.93E-09 | 5.93E-09 | mr1389_2 | 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 |