Variant ID: vg0608661476 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 8661476 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACATAGTCGTGGATGACGAGCGGTGACTCGTAGAGGCGGCGATGGAGGATCGGCAGGCAGAGTGGTCATGGTCGATGGGGATCGGCGGTGGCGTGGCTAC[G/A]
GAAGACGGGCAGTGACTCTTGGAGGCGCCGTGGGCAACGGTCGACGGGGAGAACCGGCGACATCCAACTTTGAACCGGCGACGGAGATCGGCGGCTGTGT
ACACAGCCGCCGATCTCCGTCGCCGGTTCAAAGTTGGATGTCGCCGGTTCTCCCCGTCGACCGTTGCCCACGGCGCCTCCAAGAGTCACTGCCCGTCTTC[C/T]
GTAGCCACGCCACCGCCGATCCCCATCGACCATGACCACTCTGCCTGCCGATCCTCCATCGCCGCCTCTACGAGTCACCGCTCGTCATCCACGACTATGT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 61.30% | 3.30% | 1.23% | 34.19% | NA |
All Indica | 2759 | 41.10% | 0.30% | 1.49% | 57.09% | NA |
All Japonica | 1512 | 88.40% | 9.80% | 0.93% | 0.86% | NA |
Aus | 269 | 99.30% | 0.00% | 0.37% | 0.37% | NA |
Indica I | 595 | 43.90% | 0.20% | 0.67% | 55.29% | NA |
Indica II | 465 | 21.30% | 1.50% | 1.51% | 75.70% | NA |
Indica III | 913 | 55.40% | 0.00% | 1.10% | 43.48% | NA |
Indica Intermediate | 786 | 34.20% | 0.00% | 2.54% | 63.23% | NA |
Temperate Japonica | 767 | 84.60% | 13.40% | 1.04% | 0.91% | NA |
Tropical Japonica | 504 | 93.50% | 5.00% | 0.99% | 0.60% | NA |
Japonica Intermediate | 241 | 90.00% | 8.30% | 0.41% | 1.24% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0608661476 | G -> A | LOC_Os06g15260.1 | intron_variant ; MODIFIER | silent_mutation | Average:46.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
vg0608661476 | G -> DEL | N | N | silent_mutation | Average:46.972; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0608661476 | NA | 1.66E-06 | mr1028 | 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 |
vg0608661476 | NA | 7.72E-07 | mr1186 | 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 |
vg0608661476 | 6.82E-07 | 6.82E-07 | mr1373 | 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 |
vg0608661476 | NA | 1.28E-06 | mr1616 | 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 |
vg0608661476 | NA | 1.24E-06 | mr1648 | 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 |
vg0608661476 | NA | 3.22E-06 | mr1652 | 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 |
vg0608661476 | NA | 1.44E-06 | mr1921 | 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 |