| Variant ID: vg0819104807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19104807 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCAAGCACGGAATCAGTTCTTGAGCTCATTCACGGAGACCCGCAAGGGAACACTTGTTCAAAAGTACAAAGTAAAAGTAATTGGTGATGTTCCTGGGACA[G/T]
GTTCTTCTAAGGATGGAGAAGTGAAACAAGCTCTAGATGACGCGGCTCAACCGAGTAATAAAGGTGCTGCAGATGGCTTTCAAGGAGATCAAGGTGATGG
CCATCACCTTGATCTCCTTGAAAGCCATCTGCAGCACCTTTATTACTCGGTTGAGCCGCGTCATCTAGAGCTTGTTTCACTTCTCCATCCTTAGAAGAAC[C/A]
TGTCCCAGGAACATCACCAATTACTTTTACTTTGTACTTTTGAACAAGTGTTCCCTTGCGGGTCTCCGTGAATGAGCTCAAGAACTGATTCCGTGCTTGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.10% | 2.60% | 1.38% | 1.93% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.07% | 0.07% | NA |
| All Japonica | 1512 | 84.70% | 7.70% | 2.78% | 4.89% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.52% | 0.65% | NA |
| Tropical Japonica | 504 | 66.70% | 20.00% | 6.35% | 6.94% | NA |
| Japonica Intermediate | 241 | 77.20% | 6.20% | 2.49% | 14.11% | NA |
| VI/Aromatic | 96 | 63.50% | 6.20% | 14.58% | 15.62% | NA |
| Intermediate | 90 | 92.20% | 1.10% | 6.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819104807 | G -> T | LOC_Os08g30940.1 | splice_acceptor_variant&intron_variant ; HIGH | splice_acceptor_variant | Average:28.918; most accessible tissue: Zhenshan97 root, score: 46.166 | N | N | N | N |
| vg0819104807 | G -> DEL | LOC_Os08g30940.1 | N | splice_acceptor_variant | Average:28.918; most accessible tissue: Zhenshan97 root, score: 46.166 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819104807 | 2.02E-06 | 6.30E-07 | mr1227 | 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 |
| vg0819104807 | 5.06E-06 | 5.05E-06 | mr1266 | 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 |
| vg0819104807 | NA | 6.77E-07 | mr1560 | 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 |
| vg0819104807 | NA | 5.70E-06 | mr1700 | 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 |