| Variant ID: vg1107417956 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 7417956 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTCTGTTGTTTATCTCAAATGGGTTGAAGTCTGTTTAATCAGTACGGCAAAAACCAGTGTACACAGTGATTTGAGTTAATTAAAAAAATTGTAACGGCA[G/A]
TCGTGTTTTTTCAGTTTTTTTCATCCTATACCGCCTTCCAAGTCACGTGCTATTCGACTGCTTACCCACTTGCACGAAATATTTATAATTAAAAAGTACT
AGTACTTTTTAATTATAAATATTTCGTGCAAGTGGGTAAGCAGTCGAATAGCACGTGACTTGGAAGGCGGTATAGGATGAAAAAAACTGAAAAAACACGA[C/T]
TGCCGTTACAATTTTTTTAATTAACTCAAATCACTGTGTACACTGGTTTTTGCCGTACTGATTAAACAGACTTCAACCCATTTGAGATAAACAACAGAGC
| 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 | 67.10% | 0.70% | 0.70% | 31.46% | NA |
| All Indica | 2759 | 53.00% | 0.00% | 0.91% | 46.07% | NA |
| All Japonica | 1512 | 90.30% | 2.30% | 0.33% | 7.08% | NA |
| Aus | 269 | 67.70% | 0.00% | 0.74% | 31.60% | NA |
| Indica I | 595 | 35.80% | 0.00% | 2.35% | 61.85% | NA |
| Indica II | 465 | 70.10% | 0.00% | 0.43% | 29.46% | NA |
| Indica III | 913 | 57.60% | 0.00% | 0.44% | 41.95% | NA |
| Indica Intermediate | 786 | 50.60% | 0.00% | 0.64% | 48.73% | NA |
| Temperate Japonica | 767 | 95.30% | 1.70% | 0.26% | 2.74% | NA |
| Tropical Japonica | 504 | 91.30% | 0.00% | 0.00% | 8.73% | NA |
| Japonica Intermediate | 241 | 72.20% | 9.10% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 1.11% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1107417956 | G -> A | LOC_Os11g13520.1 | upstream_gene_variant ; 4719.0bp to feature; MODIFIER | silent_mutation | Average:34.577; most accessible tissue: Callus, score: 71.289 | N | N | N | N |
| vg1107417956 | G -> A | LOC_Os11g13530.1 | downstream_gene_variant ; 1680.0bp to feature; MODIFIER | silent_mutation | Average:34.577; most accessible tissue: Callus, score: 71.289 | N | N | N | N |
| vg1107417956 | G -> A | LOC_Os11g13520-LOC_Os11g13530 | intergenic_region ; MODIFIER | silent_mutation | Average:34.577; most accessible tissue: Callus, score: 71.289 | N | N | N | N |
| vg1107417956 | G -> DEL | N | N | silent_mutation | Average:34.577; most accessible tissue: Callus, score: 71.289 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1107417956 | NA | 8.32E-06 | Grain_weight | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1107417956 | 3.99E-10 | 1.10E-07 | mr1038_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 |
| vg1107417956 | 1.31E-07 | 1.31E-07 | mr1191_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 |
| vg1107417956 | 8.27E-06 | 8.27E-06 | mr1389_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 |