| Variant ID: vg1004534495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4534495 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCTTCCGGTTCCTCCGCCACGTCCCCCTGCACCATCTCCTCCGTCTCCTCCGCCACCTCCTCCTGCACCATCTCCTCCGGCTCCTCGGCTCCTCCGCCT[C/T]
CTCCACCTCCACCGTGTCCGCCTGCACTTCCCAAGACAAGGTCTCGCCAAGCTCTACCGCCTGCCCGCACAAGGGCAACGAAGAAGGCGAAAGTTGACGC
GCGTCAACTTTCGCCTTCTTCGTTGCCCTTGTGCGGGCAGGCGGTAGAGCTTGGCGAGACCTTGTCTTGGGAAGTGCAGGCGGACACGGTGGAGGTGGAG[G/A]
AGGCGGAGGAGCCGAGGAGCCGGAGGAGATGGTGCAGGAGGAGGTGGCGGAGGAGACGGAGGAGATGGTGCAGGGGGACGTGGCGGAGGAACCGGAAGAT
| 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 | 40.80% | 6.00% | 18.54% | 34.70% | NA |
| All Indica | 2759 | 29.90% | 6.60% | 29.07% | 34.51% | NA |
| All Japonica | 1512 | 51.50% | 4.80% | 1.85% | 41.80% | NA |
| Aus | 269 | 90.30% | 1.50% | 4.46% | 3.72% | NA |
| Indica I | 595 | 35.50% | 1.20% | 29.58% | 33.78% | NA |
| Indica II | 465 | 28.00% | 7.70% | 39.35% | 24.95% | NA |
| Indica III | 913 | 26.80% | 10.40% | 24.32% | 38.44% | NA |
| Indica Intermediate | 786 | 30.30% | 5.50% | 28.12% | 36.13% | NA |
| Temperate Japonica | 767 | 80.30% | 9.30% | 0.52% | 9.91% | NA |
| Tropical Japonica | 504 | 8.50% | 0.40% | 3.77% | 87.30% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 2.07% | 48.13% | NA |
| VI/Aromatic | 96 | 40.60% | 19.80% | 11.46% | 28.12% | NA |
| Intermediate | 90 | 45.60% | 7.80% | 25.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004534495 | C -> T | LOC_Os10g08360.1 | downstream_gene_variant ; 614.0bp to feature; MODIFIER | silent_mutation | Average:14.154; most accessible tissue: Callus, score: 42.302 | N | N | N | N |
| vg1004534495 | C -> T | LOC_Os10g08370.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.154; most accessible tissue: Callus, score: 42.302 | N | N | N | N |
| vg1004534495 | C -> DEL | N | N | silent_mutation | Average:14.154; most accessible tissue: Callus, score: 42.302 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004534495 | NA | 2.22E-06 | mr1515 | 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 |
| vg1004534495 | NA | 8.95E-06 | mr1765 | 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 |
| vg1004534495 | NA | 1.39E-08 | mr1305_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 |
| vg1004534495 | 1.25E-07 | 1.25E-07 | mr1317_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 |
| vg1004534495 | NA | 3.50E-09 | mr1585_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 |
| vg1004534495 | NA | 5.13E-06 | mr1765_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 |
| vg1004534495 | 6.05E-06 | 6.05E-06 | mr1897_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 |