| Variant ID: vg0719711141 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19711141 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.61, C: 0.39, others allele: 0.00, population size: 93. )
CCCGTAGACATCCAGCAAGTGGAGACGAGAGCTCTGGCGACAACCGCGGTGAAGAAGACGACCATTGCCGCCGTTCACGGCCGGACAGGAAGCTGCCAGG[T/C]
TGCTCCGTGTGAGTCGACCAACCTTCGCCTCTGCCTCCATGTAAACACCCCTCAATCACAGTCAGGCGGCATGCCTTGTTCCATCCTTGGACGGATGAGC
GCTCATCCGTCCAAGGATGGAACAAGGCATGCCGCCTGACTGTGATTGAGGGGTGTTTACATGGAGGCAGAGGCGAAGGTTGGTCGACTCACACGGAGCA[A/G]
CCTGGCAGCTTCCTGTCCGGCCGTGAACGGCGGCAATGGTCGTCTTCTTCACCGCGGTTGTCGCCAGAGCTCTCGTCTCCACTTGCTGGATGTCTACGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.50% | 15.40% | 0.36% | 64.79% | NA |
| All Indica | 2759 | 1.80% | 2.20% | 0.43% | 95.58% | NA |
| All Japonica | 1512 | 55.20% | 42.90% | 0.20% | 1.65% | NA |
| Aus | 269 | 0.00% | 0.70% | 0.74% | 98.51% | NA |
| Indica I | 595 | 0.50% | 1.20% | 0.17% | 98.15% | NA |
| Indica II | 465 | 3.90% | 2.20% | 0.22% | 93.76% | NA |
| Indica III | 913 | 1.50% | 1.80% | 0.33% | 96.39% | NA |
| Indica Intermediate | 786 | 1.90% | 3.40% | 0.89% | 93.77% | NA |
| Temperate Japonica | 767 | 41.90% | 55.90% | 0.26% | 1.96% | NA |
| Tropical Japonica | 504 | 88.70% | 11.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 27.80% | 67.60% | 0.41% | 4.15% | NA |
| VI/Aromatic | 96 | 8.30% | 2.10% | 0.00% | 89.58% | NA |
| Intermediate | 90 | 30.00% | 15.60% | 0.00% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719711141 | T -> DEL | N | N | silent_mutation | Average:9.221; most accessible tissue: Callus, score: 42.217 | N | N | N | N |
| vg0719711141 | T -> C | LOC_Os07g33000.1 | upstream_gene_variant ; 2054.0bp to feature; MODIFIER | silent_mutation | Average:9.221; most accessible tissue: Callus, score: 42.217 | N | N | N | N |
| vg0719711141 | T -> C | LOC_Os07g32990.1 | downstream_gene_variant ; 1178.0bp to feature; MODIFIER | silent_mutation | Average:9.221; most accessible tissue: Callus, score: 42.217 | N | N | N | N |
| vg0719711141 | T -> C | LOC_Os07g32990-LOC_Os07g33000 | intergenic_region ; MODIFIER | silent_mutation | Average:9.221; most accessible tissue: Callus, score: 42.217 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0719711141 | 1.93E-09 | NA | Spikelet_length | 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 |
| vg0719711141 | 1.64E-08 | NA | Spikelet_length | Jap_All | YES | 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 |
| vg0719711141 | NA | 8.51E-06 | mr1154_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 |
| vg0719711141 | NA | 1.76E-08 | mr1821_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 |