| Variant ID: vg0712954506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12954506 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGCTGCTGTCAACACCTGGAACAAATGCTCTACATCATTCCTCTTGAAATTCTTCCCGATGGACAAAACCAATGCCCTTCGTGGAAGGATTTCCAGTTTC[T/C]
AGCAGACAAGGGACGAGTCTATTCTAGAAACATGGGAACGACTGCAGGAGTACGTGGCCGCCTGTCCTCATCATGGGATGGACGACTGGCTGATCCTGCA
TGCAGGATCAGCCAGTCGTCCATCCCATGATGAGGACAGGCGGCCACGTACTCCTGCAGTCGTTCCCATGTTTCTAGAATAGACTCGTCCCTTGTCTGCT[A/G]
GAAACTGGAAATCCTTCCACGAAGGGCATTGGTTTTGTCCATCGGGAAGAATTTCAAGAGGAATGATGTAGAGCATTTGTTCCAGGTGTTGACAGCAGCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.80% | 29.60% | 28.54% | 4.00% | NA |
| All Indica | 2759 | 15.30% | 42.80% | 39.04% | 2.83% | NA |
| All Japonica | 1512 | 81.50% | 3.40% | 8.20% | 6.81% | NA |
| Aus | 269 | 28.30% | 44.60% | 25.28% | 1.86% | NA |
| Indica I | 595 | 20.70% | 27.60% | 49.08% | 2.69% | NA |
| Indica II | 465 | 26.20% | 35.10% | 35.05% | 3.66% | NA |
| Indica III | 913 | 3.80% | 59.00% | 34.94% | 2.19% | NA |
| Indica Intermediate | 786 | 18.20% | 40.10% | 38.55% | 3.18% | NA |
| Temperate Japonica | 767 | 77.70% | 2.20% | 7.17% | 12.91% | NA |
| Tropical Japonica | 504 | 87.50% | 3.40% | 8.93% | 0.20% | NA |
| Japonica Intermediate | 241 | 81.30% | 7.50% | 9.96% | 1.24% | NA |
| VI/Aromatic | 96 | 10.40% | 28.10% | 58.33% | 3.12% | NA |
| Intermediate | 90 | 51.10% | 22.20% | 26.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712954506 | T -> DEL | N | N | silent_mutation | Average:21.218; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| vg0712954506 | T -> C | LOC_Os07g22960.1 | upstream_gene_variant ; 4423.0bp to feature; MODIFIER | silent_mutation | Average:21.218; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| vg0712954506 | T -> C | LOC_Os07g22970.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.218; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712954506 | NA | 3.29E-10 | Grain_weight | 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 |
| vg0712954506 | 9.98E-06 | 8.43E-10 | mr1524 | 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 |
| vg0712954506 | NA | 1.02E-06 | mr1761 | 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 |
| vg0712954506 | NA | 1.18E-09 | mr1790 | 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 |
| vg0712954506 | NA | 8.83E-12 | mr1986_2 | 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 |