| Variant ID: vg1110245970 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 10245970 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCAAGACGGGCGGAATGCGATATCGATACGGAGAGGAGAGCGCGACCTAGCTCCTCCAAATCGAGCACCGCTGCCACTACTCCCTCGCAGCGCACGCGT[T/C]
GCCGGCGCCGCCCCCTCTCCCCACAGACTCTGCTGCTCCCTCGTCTTGTGCGCTCCTCCAACCACCGCTTGGCCAGGCTGGCGCATCGATGCTCCCCACC
GGTGGGGAGCATCGATGCGCCAGCCTGGCCAAGCGGTGGTTGGAGGAGCGCACAAGACGAGGGAGCAGCAGAGTCTGTGGGGAGAGGGGGCGGCGCCGGC[A/G]
ACGCGTGCGCTGCGAGGGAGTAGTGGCAGCGGTGCTCGATTTGGAGGAGCTAGGTCGCGCTCTCCTCTCCGTATCGATATCGCATTCCGCCCGTCTTGGA
| 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 | 64.70% | 35.20% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 93.70% | 6.20% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.80% | 2.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 84.00% | 15.80% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.10% | 88.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 80.20% | 19.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 33.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1110245970 | T -> C | LOC_Os11g18194.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.013; most accessible tissue: Zhenshan97 young leaf, score: 89.666 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1110245970 | 4.10E-06 | NA | mr1101 | 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 |
| vg1110245970 | NA | 8.96E-11 | mr1595 | 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 |
| vg1110245970 | NA | 2.39E-08 | mr1644 | 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 |
| vg1110245970 | 7.36E-06 | 7.36E-06 | mr1918 | 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 |