| Variant ID: vg0318783105 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 18783105 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CACGGGAGGCGGCGACAAGAGGCGAATGGGAGAGGAAAGGAAAGGGGGGGAAGCTTGGGTTTATATGGGCGACAATGTCGGTTTGGGAGAGGGGAACCGA[G/C]
TTTGGACGGTCAAGCCAGCGAGCTGGCGCTCCGGCTAGCGGCCAAATCGGCGACAGGGAGGAGGGGAATGACGCCGGTGGAGGAAGAAAAAGGAAAAGGA
TCCTTTTCCTTTTTCTTCCTCCACCGGCGTCATTCCCCTCCTCCCTGTCGCCGATTTGGCCGCTAGCCGGAGCGCCAGCTCGCTGGCTTGACCGTCCAAA[C/G]
TCGGTTCCCCTCTCCCAAACCGACATTGTCGCCCATATAAACCCAAGCTTCCCCCCCTTTCCTTTCCTCTCCCATTCGCCTCTTGTCGCCGCCTCCCGTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.30% | 21.90% | 12.93% | 32.90% | NA |
| All Indica | 2759 | 3.10% | 28.80% | 16.53% | 51.58% | NA |
| All Japonica | 1512 | 85.80% | 11.80% | 1.52% | 0.79% | NA |
| Aus | 269 | 9.70% | 16.00% | 41.26% | 33.09% | NA |
| Indica I | 595 | 2.70% | 20.20% | 29.58% | 47.56% | NA |
| Indica II | 465 | 3.40% | 22.20% | 9.89% | 64.52% | NA |
| Indica III | 913 | 2.20% | 41.90% | 12.49% | 43.37% | NA |
| Indica Intermediate | 786 | 4.30% | 23.90% | 15.27% | 56.49% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 65.30% | 31.30% | 1.98% | 1.39% | NA |
| Japonica Intermediate | 241 | 85.10% | 8.70% | 5.39% | 0.83% | NA |
| VI/Aromatic | 96 | 72.90% | 6.20% | 13.54% | 7.29% | NA |
| Intermediate | 90 | 51.10% | 13.30% | 8.89% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0318783105 | G -> C | LOC_Os03g32840.1 | upstream_gene_variant ; 2972.0bp to feature; MODIFIER | silent_mutation | Average:39.973; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0318783105 | G -> C | LOC_Os03g32820.1 | downstream_gene_variant ; 3144.0bp to feature; MODIFIER | silent_mutation | Average:39.973; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0318783105 | G -> C | LOC_Os03g32830.1 | downstream_gene_variant ; 529.0bp to feature; MODIFIER | silent_mutation | Average:39.973; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0318783105 | G -> C | LOC_Os03g32820-LOC_Os03g32830 | intergenic_region ; MODIFIER | silent_mutation | Average:39.973; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0318783105 | G -> DEL | N | N | silent_mutation | Average:39.973; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0318783105 | NA | 3.08E-07 | mr1227 | 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 |
| vg0318783105 | 6.51E-06 | NA | mr1055_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 |
| vg0318783105 | 3.93E-07 | NA | mr1390_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 |
| vg0318783105 | 4.62E-07 | NA | mr1490_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 |