| Variant ID: vg1120641607 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20641607 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGAACTTCTTCCTGTAAACAAGCAACAGCCAACGCAGATTCGAGATTTTGTGGACGCTGAAGCAAAACAGCATTTCTAATTTCCCTTTTTAAACCCTCT[G/A]
TAAACTTATGGGTTAAGTACTTGGTGCTAACCACCGGATCATAAACATCAGTTGATTCATCAATTCATCAAAACGCTCATAAAACTCCCAAACAGTGCTG
CAGCACTGTTTGGGAGTTTTATGAGCGTTTTGATGAATTGATGAATCAACTGATGTTTATGATCCGGTGGTTAGCACCAAGTACTTAACCCATAAGTTTA[C/T]
AGAGGGTTTAAAAAGGGAAATTAGAAATGCTGTTTTGCTTCAGCGTCCACAAAATCTCGAATCTGCGTTGGCTGTTGCTTGTTTACAGGAAGAAGTTCTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 0.60% | 0.70% | 5.01% | NA |
| All Indica | 2759 | 98.20% | 0.00% | 0.11% | 1.70% | NA |
| All Japonica | 1512 | 91.90% | 1.70% | 1.65% | 4.83% | NA |
| Aus | 269 | 56.10% | 0.00% | 1.86% | 42.01% | NA |
| Indica I | 595 | 99.00% | 0.00% | 0.00% | 1.01% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.00% | 0.00% | 0.33% | 2.63% | NA |
| Indica Intermediate | 786 | 97.80% | 0.00% | 0.00% | 2.16% | NA |
| Temperate Japonica | 767 | 89.80% | 3.30% | 2.22% | 4.69% | NA |
| Tropical Japonica | 504 | 91.70% | 0.00% | 1.59% | 6.75% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120641607 | G -> A | LOC_Os11g35210.1 | upstream_gene_variant ; 1777.0bp to feature; MODIFIER | silent_mutation | Average:37.223; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg1120641607 | G -> A | LOC_Os11g35200.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.223; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg1120641607 | G -> DEL | N | N | silent_mutation | Average:37.223; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1120641607 | NA | 2.26E-06 | mr1210 | 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 |
| vg1120641607 | NA | 4.13E-06 | mr1305 | 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 |
| vg1120641607 | NA | 5.35E-08 | mr1585 | 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 |
| vg1120641607 | NA | 1.83E-06 | mr1586 | 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 |
| vg1120641607 | 1.25E-06 | 1.25E-06 | mr1587 | 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 |
| vg1120641607 | NA | 5.15E-06 | 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 |
| vg1120641607 | NA | 9.23E-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 |