| Variant ID: vg0321811921 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21811921 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACCCAATAGTTTCCCGACTGACTGACGAATAAACTCCAAATAAAATTTTACTAAAACCCTAGACTAAGCTAATTTTAAAGATCCGATCCGAATGAACGA[C/T]
CAAGATTTTTCCCACAAACCAAAGAGGCAAAACACCAAATTTTTTCCGAAACAAATCCAAGTGCAAAGAGCATATGCAGATGAAAAGGGGATCAAAGGGC
GCCCTTTGATCCCCTTTTCATCTGCATATGCTCTTTGCACTTGGATTTGTTTCGGAAAAAATTTGGTGTTTTGCCTCTTTGGTTTGTGGGAAAAATCTTG[G/A]
TCGTTCATTCGGATCGGATCTTTAAAATTAGCTTAGTCTAGGGTTTTAGTAAAATTTTATTTGGAGTTTATTCGTCAGTCAGTCGGGAAACTATTGGGTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.80% | 3.10% | 1.82% | 0.30% | NA |
| All Indica | 2759 | 98.70% | 0.30% | 1.01% | 0.00% | NA |
| All Japonica | 1512 | 86.50% | 9.00% | 3.64% | 0.86% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.30% | 1.51% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 0.80% | 2.04% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 65.30% | 24.20% | 8.33% | 2.18% | NA |
| Japonica Intermediate | 241 | 90.50% | 5.40% | 3.32% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 2.20% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0321811921 | C -> T | LOC_Os03g39250.1 | upstream_gene_variant ; 641.0bp to feature; MODIFIER | silent_mutation | Average:10.237; most accessible tissue: Callus, score: 33.367 | N | N | N | N |
| vg0321811921 | C -> T | LOC_Os03g39270.1 | downstream_gene_variant ; 4215.0bp to feature; MODIFIER | silent_mutation | Average:10.237; most accessible tissue: Callus, score: 33.367 | N | N | N | N |
| vg0321811921 | C -> T | LOC_Os03g39250-LOC_Os03g39270 | intergenic_region ; MODIFIER | silent_mutation | Average:10.237; most accessible tissue: Callus, score: 33.367 | N | N | N | N |
| vg0321811921 | C -> DEL | N | N | silent_mutation | Average:10.237; most accessible tissue: Callus, score: 33.367 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0321811921 | NA | 3.36E-06 | 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 |
| vg0321811921 | NA | 2.49E-06 | mr1083 | 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 |
| vg0321811921 | 1.75E-06 | 1.75E-06 | mr1335_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 |