| Variant ID: vg1122905780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 22905780 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAACTAATGGTAAAATGCCAATTTGCAGATCATGCTTTACAAAAATAAATGTAGGGTCTAAAAATTTAGGTTTACAAAATGCACTATAAAAATAATTATA[G/T]
ATACTAATTTTTTGTTGTACCATACAAAAGCTGAGTCTATAATTTTGTTTTCTGTTGGCGCTACCTTCGATTGATTGCATTTTCTGATTCCTTAAATTAT
ATAATTTAAGGAATCAGAAAATGCAATCAATCGAAGGTAGCGCCAACAGAAAACAAAATTATAGACTCAGCTTTTGTATGGTACAACAAAAAATTAGTAT[C/A]
TATAATTATTTTTATAGTGCATTTTGTAAACCTAAATTTTTAGACCCTACATTTATTTTTGTAAAGCATGATCTGCAAATTGGCATTTTACCATTAGTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.00% | 34.80% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 85.70% | 14.10% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 25.50% | 74.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 70.30% | 29.20% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 9.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 13.80% | 86.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 32.70% | 67.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 47.30% | 52.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 17.70% | 82.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1122905780 | G -> T | LOC_Os11g38640.1 | upstream_gene_variant ; 4906.0bp to feature; MODIFIER | silent_mutation | Average:22.106; most accessible tissue: Callus, score: 59.614 | N | N | N | N |
| vg1122905780 | G -> T | LOC_Os11g38630.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.106; most accessible tissue: Callus, score: 59.614 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1122905780 | NA | 5.32E-10 | mr1128 | 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 |
| vg1122905780 | 7.58E-07 | 7.58E-07 | mr1336 | 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 |
| vg1122905780 | NA | 9.31E-13 | mr1128_2 | 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 |