| Variant ID: vg0723501936 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 23501936 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATTTCCACGTATTGAACTCTTTTCCAAATACGAATGAGTACCCTGGCATTTCGCTCTTTCTAAATCTCCCATGCGACGAGGATCACCATCGAGTCAAGCA[G/C]
TTTTCTCTGTTCTTTGTGAACCTTCTTCCGGACTTCGTATCACCCAGCAAAAGAGACCATCTCCTGTGAAAACATCACCGTTCCTATCCGTTGGCAGATT
AATCTGCCAACGGATAGGAACGGTGATGTTTTCACAGGAGATGGTCTCTTTTGCTGGGTGATACGAAGTCCGGAAGAAGGTTCACAAAGAACAGAGAAAA[C/G]
TGCTTGACTCGATGGTGATCCTCGTCGCATGGGAGATTTAGAAAGAGCGAAATGCCAGGGTACTCATTCGTATTTGGAAAAGAGTTCAATACGTGGAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.20% | 28.00% | 1.06% | 17.75% | NA |
| All Indica | 2759 | 87.00% | 4.70% | 0.58% | 7.72% | NA |
| All Japonica | 1512 | 1.40% | 59.10% | 1.65% | 37.90% | NA |
| Aus | 269 | 23.00% | 76.60% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.00% | 3.90% | 0.00% | 1.18% | NA |
| Indica II | 465 | 88.00% | 3.40% | 1.29% | 7.31% | NA |
| Indica III | 913 | 86.30% | 1.90% | 0.77% | 11.06% | NA |
| Indica Intermediate | 786 | 81.00% | 9.50% | 0.38% | 9.03% | NA |
| Temperate Japonica | 767 | 0.80% | 87.20% | 0.13% | 11.86% | NA |
| Tropical Japonica | 504 | 2.00% | 27.00% | 3.57% | 67.46% | NA |
| Japonica Intermediate | 241 | 2.10% | 36.50% | 2.49% | 58.92% | NA |
| VI/Aromatic | 96 | 1.00% | 64.60% | 1.04% | 33.33% | NA |
| Intermediate | 90 | 35.60% | 33.30% | 7.78% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0723501936 | G -> DEL | N | N | silent_mutation | Average:70.392; most accessible tissue: Callus, score: 97.52 | N | N | N | N |
| vg0723501936 | G -> C | LOC_Os07g39250.1 | upstream_gene_variant ; 1649.0bp to feature; MODIFIER | silent_mutation | Average:70.392; most accessible tissue: Callus, score: 97.52 | N | N | N | N |
| vg0723501936 | G -> C | LOC_Os07g39260.1 | downstream_gene_variant ; 978.0bp to feature; MODIFIER | silent_mutation | Average:70.392; most accessible tissue: Callus, score: 97.52 | N | N | N | N |
| vg0723501936 | G -> C | LOC_Os07g39270.1 | downstream_gene_variant ; 4916.0bp to feature; MODIFIER | silent_mutation | Average:70.392; most accessible tissue: Callus, score: 97.52 | N | N | N | N |
| vg0723501936 | G -> C | LOC_Os07g39250-LOC_Os07g39260 | intergenic_region ; MODIFIER | silent_mutation | Average:70.392; most accessible tissue: Callus, score: 97.52 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0723501936 | NA | 3.37E-06 | Awn_length | 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 |
| vg0723501936 | NA | 1.59E-21 | mr1155 | 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 |
| vg0723501936 | 1.97E-06 | NA | mr1563 | 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 |
| vg0723501936 | 4.86E-10 | NA | mr1563_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 |
| vg0723501936 | 4.66E-06 | 1.63E-11 | mr1563_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 |