| Variant ID: vg1204356347 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4356347 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CACCAAGTTCTCCTATCTGGCGCGGCACTGTCGATGGGGGATACCCGTAGACCAGATATAGAGGGTATTGGGGTCCGTTGGTACGAGGATCTACGTAGTA[C/T]
GACATCAGGCAAACAAAAGACAAGGATTATACTGGTTTAGGCCCCTTAGTAGGTAATAGCCCTAATCCAGTTGGTATGGGATTATATGATGGAATCCACA
TGTGGATTCCATCATATAATCCCATACCAACTGGATTAGGGCTATTACCTACTAAGGGGCCTAAACCAGTATAATCCTTGTCTTTTGTTTGCCTGATGTC[G/A]
TACTACGTAGATCCTCGTACCAACGGACCCCAATACCCTCTATATCTGGTCTACGGGTATCCCCCATCGACAGTGCCGCGCCAGATAGGAGAACTTGGTG
| 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 | 56.50% | 0.10% | 10.83% | 32.54% | NA |
| All Indica | 2759 | 54.00% | 0.20% | 14.75% | 31.06% | NA |
| All Japonica | 1512 | 58.30% | 0.00% | 2.31% | 39.42% | NA |
| Aus | 269 | 77.30% | 0.00% | 13.01% | 9.67% | NA |
| Indica I | 595 | 61.00% | 0.00% | 7.39% | 31.60% | NA |
| Indica II | 465 | 53.50% | 0.00% | 18.49% | 27.96% | NA |
| Indica III | 913 | 47.90% | 0.30% | 17.74% | 34.06% | NA |
| Indica Intermediate | 786 | 56.00% | 0.40% | 14.63% | 29.01% | NA |
| Temperate Japonica | 767 | 81.60% | 0.00% | 1.43% | 16.95% | NA |
| Tropical Japonica | 504 | 31.30% | 0.00% | 3.57% | 65.08% | NA |
| Japonica Intermediate | 241 | 40.20% | 0.00% | 2.49% | 57.26% | NA |
| VI/Aromatic | 96 | 40.60% | 0.00% | 20.83% | 38.54% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 16.67% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204356347 | C -> DEL | LOC_Os12g08580.1 | N | frameshift_variant | Average:26.36; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| vg1204356347 | C -> T | LOC_Os12g08580.1 | synonymous_variant ; p.Ser2Ser; LOW | synonymous_codon | Average:26.36; most accessible tissue: Minghui63 panicle, score: 53.77 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204356347 | NA | 9.86E-06 | mr1134 | 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 |
| vg1204356347 | 7.41E-06 | 4.79E-06 | mr1135 | 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 |
| vg1204356347 | 3.71E-07 | 3.71E-07 | mr1778 | Ind_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 |