| Variant ID: vg1013347408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 13347408 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.02, others allele: 0.00, population size: 236. )
GAGCATGCCTTCTTTCCTTTTATAGTTTGTCCGGAAAGATTACCGAGTGCAGGGTAGTCATTAATGGTGCACAACAATAGAACTCTTAGCTTGAAGTTCT[C/A]
CTGACCATATGCATCCCAAGTTTCCACACCTTCTTTCCAAAGAATCTCCAGATCGTCGATAACAGGCTCCAGGAATACATCCATATCATTGCCGGGTTGC
GCAACCCGGCAATGATATGGATGTATTCCTGGAGCCTGTTATCGACGATCTGGAGATTCTTTGGAAAGAAGGTGTGGAAACTTGGGATGCATATGGTCAG[G/T]
AGAACTTCAAGCTAAGAGTTCTATTGTTGTGCACCATTAATGACTACCCTGCACTCGGTAATCTTTCCGGACAAACTATAAAAGGAAAGAAGGCATGCTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.70% | 28.10% | 11.09% | 0.08% | NA |
| All Indica | 2759 | 81.70% | 3.80% | 14.35% | 0.14% | NA |
| All Japonica | 1512 | 24.10% | 72.40% | 3.44% | 0.00% | NA |
| Aus | 269 | 73.60% | 3.00% | 23.42% | 0.00% | NA |
| Indica I | 595 | 85.90% | 1.20% | 12.94% | 0.00% | NA |
| Indica II | 465 | 77.20% | 5.20% | 17.63% | 0.00% | NA |
| Indica III | 913 | 82.00% | 4.30% | 13.58% | 0.11% | NA |
| Indica Intermediate | 786 | 80.90% | 4.30% | 14.38% | 0.38% | NA |
| Temperate Japonica | 767 | 4.80% | 94.10% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 47.80% | 47.80% | 4.37% | 0.00% | NA |
| Japonica Intermediate | 241 | 36.10% | 54.80% | 9.13% | 0.00% | NA |
| VI/Aromatic | 96 | 15.60% | 80.20% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 50.00% | 10.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1013347408 | C -> A | LOC_Os10g25760.1 | stop_gained ; p.Glu351*; HIGH | stop_gained | Average:14.496; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| vg1013347408 | C -> DEL | LOC_Os10g25760.1 | N | frameshift_variant | Average:14.496; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013347408 | 3.53E-06 | NA | mr1533 | 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 |
| vg1013347408 | 2.76E-06 | 3.31E-12 | mr1533 | 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 |
| vg1013347408 | 9.63E-06 | NA | mr1980 | 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 |
| vg1013347408 | NA | 1.08E-13 | mr1980 | 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 |
| vg1013347408 | NA | 5.97E-06 | mr1155_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 |
| vg1013347408 | 3.00E-06 | 1.25E-15 | mr1533_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 |
| vg1013347408 | NA | 3.16E-07 | mr1980_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 |