| Variant ID: vg0713895671 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13895671 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGAGAAGTGCCGAGAGTTGATGAACGAATTTCGGCTGGTGACTTTGAAGCATGTATCTCGAGAACAGAATGTTGAAGCTAATGATTTGGCCCAAGGGGC[A/G]
TCGGGATATAAGCCGATGATGAAGGATGTCAAAGTAGAAGTTGCCACATTAACAGCCGATGATTGGAGGTATGATGTGCATCATTATTTGCATAATCCAT
ATGGATTATGCAAATAATGATGCACATCATACCTCCAATCATCGGCTGTTAATGTGGCAACTTCTACTTTGACATCCTTCATCATCGGCTTATATCCCGA[T/C]
GCCCCTTGGGCCAAATCATTAGCTTCAACATTCTGTTCTCGAGATACATGCTTCAAAGTCACCAGCCGAAATTCGTTCATCAACTCTCGGCACTTCTCAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.90% | 1.10% | 1.93% | 7.11% | NA |
| All Indica | 2759 | 87.10% | 1.30% | 2.65% | 8.95% | NA |
| All Japonica | 1512 | 93.40% | 0.50% | 0.99% | 5.16% | NA |
| Aus | 269 | 92.90% | 3.00% | 0.37% | 3.72% | NA |
| Indica I | 595 | 93.60% | 1.80% | 2.02% | 2.52% | NA |
| Indica II | 465 | 94.40% | 0.20% | 2.15% | 3.23% | NA |
| Indica III | 913 | 79.10% | 0.40% | 3.18% | 17.31% | NA |
| Indica Intermediate | 786 | 87.00% | 2.70% | 2.80% | 7.51% | NA |
| Temperate Japonica | 767 | 95.70% | 0.90% | 0.39% | 3.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.00% | 1.19% | 1.19% | NA |
| Japonica Intermediate | 241 | 77.20% | 0.00% | 2.49% | 20.33% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713895671 | A -> DEL | LOC_Os07g24400.1 | N | frameshift_variant | Average:31.309; most accessible tissue: Zhenshan97 young leaf, score: 47.311 | N | N | N | N |
| vg0713895671 | A -> G | LOC_Os07g24400.1 | synonymous_variant ; p.Ala623Ala; LOW | synonymous_codon | Average:31.309; most accessible tissue: Zhenshan97 young leaf, score: 47.311 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713895671 | 6.60E-06 | 6.59E-06 | mr1369_2 | Ind_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 |
| vg0713895671 | 3.32E-06 | 3.32E-06 | mr1453_2 | Ind_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 |
| vg0713895671 | NA | 9.14E-07 | mr1624_2 | Ind_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 |
| vg0713895671 | NA | 9.43E-06 | mr1811_2 | Ind_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 |