Variant ID: vg0716554289 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 16554289 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CACCATCACGCCCACCCTTGCCTGGATGCGTCAACTAGAGGAAAGCTACACTACAAGCCCAGCCGTTGCCCACGCTAGCTTGTGGTAAGTACGAGGAATT[G/C]
TTCTAGGGTTTCCCGCGAACCGGTCCTCAAGTGCCATGGGCGCGACCATCACAACCATGCACCCACAGCCCACTAGATGGTATATTTTAATTGACTAACA
TGTTAGTCAATTAAAATATACCATCTAGTGGGCTGTGGGTGCATGGTTGTGATGGTCGCGCCCATGGCACTTGAGGACCGGTTCGCGGGAAACCCTAGAA[C/G]
AATTCCTCGTACTTACCACAAGCTAGCGTGGGCAACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGTTGACGCATCCAGGCAAGGGTGGGCGTGATGGTG
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 44.00% | 7.40% | 8.74% | 39.89% | NA |
All Indica | 2759 | 25.10% | 1.90% | 12.03% | 60.93% | NA |
All Japonica | 1512 | 80.40% | 18.30% | 0.73% | 0.60% | NA |
Aus | 269 | 15.60% | 4.50% | 20.82% | 59.11% | NA |
Indica I | 595 | 45.20% | 0.20% | 5.38% | 49.24% | NA |
Indica II | 465 | 7.30% | 0.40% | 9.46% | 82.80% | NA |
Indica III | 913 | 19.20% | 0.80% | 18.18% | 61.88% | NA |
Indica Intermediate | 786 | 27.40% | 5.50% | 11.45% | 55.73% | NA |
Temperate Japonica | 767 | 93.90% | 4.60% | 0.91% | 0.65% | NA |
Tropical Japonica | 504 | 56.70% | 42.50% | 0.60% | 0.20% | NA |
Japonica Intermediate | 241 | 87.10% | 11.20% | 0.41% | 1.24% | NA |
VI/Aromatic | 96 | 85.40% | 0.00% | 11.46% | 3.12% | NA |
Intermediate | 90 | 50.00% | 10.00% | 3.33% | 36.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0716554289 | G -> DEL | N | N | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 | N | N | N | N |
vg0716554289 | G -> C | LOC_Os07g28350.1 | downstream_gene_variant ; 4310.0bp to feature; MODIFIER | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 | N | N | N | N |
vg0716554289 | G -> C | LOC_Os07g28360.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0716554289 | 1.62E-07 | NA | mr1705_2 | 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 |
vg0716554289 | 1.59E-06 | 7.34E-10 | mr1705_2 | Ind_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 |