| Variant ID: vg0716578471 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 16578471 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGGTATATCGCTCCATGATTGGATCTTTGCTTCACTTATGTGCATCTCGTCCTGACATCATGCTTAGTGTTTCCATGTGTGCCCGTTTTCAAGCGGAGCC[T/A]
AAAGAGTGCCATTTGATTGCCGTCAAGAGAATTCTAAGATATTTAGTTCATACTCCTAATCTTGGCTTGTGGTATCCTAAGGGTTGTGACTTTAAGCTTT
AAAGCTTAAAGTCACAACCCTTAGGATACCACAAGCCAAGATTAGGAGTATGAACTAAATATCTTAGAATTCTCTTGACGGCAATCAAATGGCACTCTTT[A/T]
GGCTCCGCTTGAAAACGGGCACACATGGAAACACTAAGCATGATGTCAGGACGAGATGCACATAAGTGAAGCAAAGATCCAATCATGGAGCGATATACCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.10% | 1.20% | 2.12% | 6.60% | NA |
| All Indica | 2759 | 86.30% | 0.00% | 2.61% | 11.05% | NA |
| All Japonica | 1512 | 94.40% | 3.80% | 1.65% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 0.67% | 0.34% | NA |
| Indica II | 465 | 60.40% | 0.00% | 6.67% | 32.90% | NA |
| Indica III | 913 | 88.70% | 0.00% | 2.08% | 9.20% | NA |
| Indica Intermediate | 786 | 89.30% | 0.00% | 2.29% | 8.40% | NA |
| Temperate Japonica | 767 | 89.20% | 7.60% | 3.13% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 3.33% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0716578471 | T -> DEL | LOC_Os07g28370.1 | N | frameshift_variant | Average:22.743; most accessible tissue: Zhenshan97 root, score: 54.262 | N | N | N | N |
| vg0716578471 | T -> A | LOC_Os07g28370.1 | synonymous_variant ; p.Pro1278Pro; LOW | synonymous_codon | Average:22.743; most accessible tissue: Zhenshan97 root, score: 54.262 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0716578471 | NA | 2.75E-12 | Heading_date | 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 |
| vg0716578471 | NA | 9.43E-08 | mr1354 | 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 |
| vg0716578471 | NA | 1.22E-09 | mr1757 | 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 |
| vg0716578471 | 4.88E-06 | 4.88E-06 | mr1193_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 |
| vg0716578471 | NA | 4.58E-09 | mr1549_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 |
| vg0716578471 | NA | 2.48E-09 | mr1757_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 |
| vg0716578471 | NA | 2.15E-06 | mr1780_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 |