| Variant ID: vg0721416115 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21416115 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 72. )
TCATACCTTCAAATCAATAATTCTTTTCTAAAAGGAAATCAGCAATTGTTCAAAAGTTACCTGTGAACTACTACTCTCCCGTCCCAAAATATAAAGAATT[A/T]
TGGGTGGATGTGATATATTTTAGCCTGTTCAGATTCGTAGTACTGGAATGTATTATATTCACTTAAATTTTTTATATTTTGGGATGGAGGGAGTACCATC
GATGGTACTCCCTCCATCCCAAAATATAAAAAATTTAAGTGAATATAATACATTCCAGTACTACGAATCTGAACAGGCTAAAATATATCACATCCACCCA[T/A]
AATTCTTTATATTTTGGGACGGGAGAGTAGTAGTTCACAGGTAACTTTTGAACAATTGCTGATTTCCTTTTAGAAAAGAATTATTGATTTGAAGGTATGA
| 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 | 52.20% | 25.80% | 1.06% | 20.99% | NA |
| All Indica | 2759 | 49.10% | 18.80% | 0.87% | 31.21% | NA |
| All Japonica | 1512 | 66.20% | 29.40% | 1.26% | 3.11% | NA |
| Aus | 269 | 14.10% | 59.50% | 1.12% | 25.28% | NA |
| Indica I | 595 | 20.80% | 8.40% | 1.01% | 69.75% | NA |
| Indica II | 465 | 67.70% | 17.20% | 1.08% | 13.98% | NA |
| Indica III | 913 | 50.10% | 30.80% | 0.77% | 18.40% | NA |
| Indica Intermediate | 786 | 58.30% | 13.90% | 0.76% | 27.10% | NA |
| Temperate Japonica | 767 | 55.80% | 42.50% | 0.65% | 1.04% | NA |
| Tropical Japonica | 504 | 80.60% | 11.30% | 2.78% | 5.36% | NA |
| Japonica Intermediate | 241 | 69.30% | 25.70% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 32.30% | 61.50% | 1.04% | 5.21% | NA |
| Intermediate | 90 | 46.70% | 37.80% | 3.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721416115 | A -> DEL | N | N | silent_mutation | Average:18.536; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
| vg0721416115 | A -> T | LOC_Os07g35740.1 | upstream_gene_variant ; 4428.0bp to feature; MODIFIER | silent_mutation | Average:18.536; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
| vg0721416115 | A -> T | LOC_Os07g35750.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.536; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
| vg0721416115 | A -> T | LOC_Os07g35750.2 | intron_variant ; MODIFIER | silent_mutation | Average:18.536; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0721416115 | NA | 3.43E-07 | Grain_weight | Ind_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 |
| vg0721416115 | 1.49E-06 | 1.49E-06 | mr1850 | 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 |
| vg0721416115 | NA | 2.06E-06 | mr1510_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 |