| Variant ID: vg0209789548 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9789548 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTGTGTTACCAACCGGGACTAAAGATCATCTTTAGTCCCGGTTCGAATGCTGTCAGGACCTGTCAGGCCCCCCCGGGATCTTTAGTCCCGGTTGGTAACA[T/C]
CAACCGGGACTAAAGATCTTAACTTTAGTCCCGGTTGGTATTACCAACCGGGACTAAAGATCCCGGTGATCTTTAGCCCCGGTTGGTGTTACCAACCGGG
CCCGGTTGGTAACACCAACCGGGGCTAAAGATCACCGGGATCTTTAGTCCCGGTTGGTAATACCAACCGGGACTAAAGTTAAGATCTTTAGTCCCGGTTG[A/G]
TGTTACCAACCGGGACTAAAGATCCCGGGGGGGCCTGACAGGTCCTGACAGCATTCGAACCGGGACTAAAGATGATCTTTAGTCCCGGTTGGTAACACAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.80% | 1.70% | 2.03% | 31.42% | NA |
| All Indica | 2759 | 51.90% | 0.00% | 2.14% | 45.99% | NA |
| All Japonica | 1512 | 91.50% | 5.40% | 2.18% | 0.99% | NA |
| Aus | 269 | 37.50% | 0.00% | 0.00% | 62.45% | NA |
| Indica I | 595 | 57.30% | 0.00% | 1.85% | 40.84% | NA |
| Indica II | 465 | 49.70% | 0.00% | 1.51% | 48.82% | NA |
| Indica III | 913 | 52.00% | 0.00% | 1.31% | 46.66% | NA |
| Indica Intermediate | 786 | 48.90% | 0.00% | 3.69% | 47.46% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 78.60% | 14.70% | 5.75% | 0.99% | NA |
| Japonica Intermediate | 241 | 95.40% | 2.90% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 71.10% | 1.10% | 4.44% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209789548 | T -> DEL | N | N | silent_mutation | Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg0209789548 | T -> C | LOC_Os02g17100.1 | upstream_gene_variant ; 756.0bp to feature; MODIFIER | silent_mutation | Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg0209789548 | T -> C | LOC_Os02g17090-LOC_Os02g17100 | intergenic_region ; MODIFIER | silent_mutation | Average:15.817; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209789548 | NA | 5.45E-06 | mr1218 | 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 |
| vg0209789548 | NA | 7.35E-06 | mr1382 | 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 |
| vg0209789548 | NA | 9.38E-07 | mr1398 | 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 |
| vg0209789548 | 1.67E-06 | 3.84E-10 | mr1422 | 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 |
| vg0209789548 | NA | 3.27E-06 | mr1583 | 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 |
| vg0209789548 | NA | 1.70E-07 | mr1696 | 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 |
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