| Variant ID: vg0719520013 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19520013 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGGTCTAGGATGGCCAATGGTGGGCCATCGACATGGCGAAGCCACGTGCTACCAGAGGTTGTTAGGTTGGCAGAGCTTTGGAGTGAGACAGCATATGTG[G/A]
GAGAGGTTGCTACAGGCAAAATACTAACTCAAGAAGTACCAGCTGGAGTTAGGGTCTGGGCGGCACCCAGGCGACTGGGTTGCGGCAGCCTTCTCCTCCC
GGGAGGAGAAGGCTGCCGCAACCCAGTCGCCTGGGTGCCGCCCAGACCCTAACTCCAGCTGGTACTTCTTGAGTTAGTATTTTGCCTGTAGCAACCTCTC[C/T]
CACATATGCTGTCTCACTCCAAAGCTCTGCCAACCTAACAACCTCTGGTAGCACGTGGCTTCGCCATGTCGATGGCCCACCATTGGCCATCCTAGACCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.30% | 8.40% | 5.12% | 7.15% | NA |
| All Indica | 2759 | 84.20% | 6.30% | 4.78% | 4.75% | NA |
| All Japonica | 1512 | 73.60% | 10.80% | 5.56% | 10.05% | NA |
| Aus | 269 | 87.70% | 6.70% | 1.12% | 4.46% | NA |
| Indica I | 595 | 91.10% | 1.80% | 5.88% | 1.18% | NA |
| Indica II | 465 | 98.10% | 0.90% | 0.43% | 0.65% | NA |
| Indica III | 913 | 76.10% | 11.80% | 3.72% | 8.32% | NA |
| Indica Intermediate | 786 | 80.20% | 6.40% | 7.76% | 5.73% | NA |
| Temperate Japonica | 767 | 97.30% | 0.70% | 1.17% | 0.91% | NA |
| Tropical Japonica | 504 | 45.80% | 21.80% | 10.32% | 22.02% | NA |
| Japonica Intermediate | 241 | 56.40% | 19.90% | 9.54% | 14.11% | NA |
| VI/Aromatic | 96 | 13.50% | 39.60% | 15.62% | 31.25% | NA |
| Intermediate | 90 | 71.10% | 5.60% | 8.89% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719520013 | G -> DEL | N | N | silent_mutation | Average:45.239; most accessible tissue: Callus, score: 62.476 | N | N | N | N |
| vg0719520013 | G -> A | LOC_Os07g32680.1 | downstream_gene_variant ; 3700.0bp to feature; MODIFIER | silent_mutation | Average:45.239; most accessible tissue: Callus, score: 62.476 | N | N | N | N |
| vg0719520013 | G -> A | LOC_Os07g32690.1 | intron_variant ; MODIFIER | silent_mutation | Average:45.239; most accessible tissue: Callus, score: 62.476 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719520013 | NA | 5.08E-06 | mr1155 | Ind_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 |
| vg0719520013 | NA | 1.05E-06 | mr1213 | 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 |
| vg0719520013 | NA | 6.69E-06 | mr1088_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 |
| vg0719520013 | NA | 1.24E-06 | mr1206_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 |
| vg0719520013 | NA | 1.69E-06 | mr1224_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 |
| vg0719520013 | NA | 8.08E-08 | mr1246_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 |
| vg0719520013 | 3.87E-06 | NA | mr1253_2 | 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 |
| vg0719520013 | NA | 1.32E-07 | mr1404_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 |
| vg0719520013 | 5.05E-06 | 3.82E-07 | mr1620_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 |