| Variant ID: vg0908369264 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8369264 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCCTTGGTAGGTAATAGCCCTAATCCAGTTGGTATGGGATTATATGATGGAAACCACGGATTACAAAGGGAATAACAGAACTCGATGATACCGACGAGAC[T/C]
ATAGTCGAGTTGGTTCGACTAGATCACTCGGCGACTTGGCTCCTGTAGGCTTCGGCTTCGTAGGCTGTGGTGGATGTGTTGGCGGTGAGATTCGATGCCT
AGGCATCGAATCTCACCGCCAACACATCCACCACAGCCTACGAAGCCGAAGCCTACAGGAGCCAAGTCGCCGAGTGATCTAGTCGAACCAACTCGACTAT[A/G]
GTCTCGTCGGTATCATCGAGTTCTGTTATTCCCTTTGTAATCCGTGGTTTCCATCATATAATCCCATACCAACTGGATTAGGGCTATTACCTACCAAGGG
| 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 | 56.00% | 1.30% | 0.61% | 42.09% | NA |
| All Indica | 2759 | 48.80% | 1.30% | 0.62% | 49.26% | NA |
| All Japonica | 1512 | 72.50% | 0.10% | 0.40% | 26.98% | NA |
| Aus | 269 | 27.10% | 7.80% | 1.49% | 63.57% | NA |
| Indica I | 595 | 52.80% | 0.00% | 0.84% | 46.39% | NA |
| Indica II | 465 | 72.90% | 6.00% | 0.43% | 20.65% | NA |
| Indica III | 913 | 30.00% | 0.30% | 0.55% | 69.11% | NA |
| Indica Intermediate | 786 | 53.30% | 0.80% | 0.64% | 45.29% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 44.20% | 0.40% | 0.99% | 54.37% | NA |
| Japonica Intermediate | 241 | 57.30% | 0.00% | 0.00% | 42.74% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 1.04% | 32.29% | NA |
| Intermediate | 90 | 75.60% | 1.10% | 1.11% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908369264 | T -> DEL | N | N | silent_mutation | Average:42.42; most accessible tissue: Minghui63 flag leaf, score: 77.828 | N | N | N | N |
| vg0908369264 | T -> C | LOC_Os09g14130.1 | upstream_gene_variant ; 2923.0bp to feature; MODIFIER | silent_mutation | Average:42.42; most accessible tissue: Minghui63 flag leaf, score: 77.828 | N | N | N | N |
| vg0908369264 | T -> C | LOC_Os09g14120.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.42; most accessible tissue: Minghui63 flag leaf, score: 77.828 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0908369264 | NA | 7.77E-06 | mr1970 | 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 |
| vg0908369264 | NA | 1.82E-07 | mr1973 | 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 |
| vg0908369264 | NA | 4.68E-08 | mr1970_2 | 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 |
| vg0908369264 | 3.72E-07 | NA | mr1973_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 |
| vg0908369264 | NA | 1.03E-10 | mr1973_2 | 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 |