Variant ID: vg0609473231 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 9473231 |
Reference Allele: G | Alternative Allele: A,C |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGGGCATCTGACAATCTTCCACCAACTTACTAAACTTCTCAAAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTTATGCAACATTGTAGATAGACATT[G/A,C]
AGTGTCCAAATCTATGGTATCTCCACCTAACGGAGAAGGTACGAACATGCCTTCTCGAGCTGCGGCGGTGTTCTCTACATCCTGATCCAACACTTCTTCA
TGAAGAAGTGTTGGATCAGGATGTAGAGAACACCGCCGCAGCTCGAGAAGGCATGTTCGTACCTTCTCCGTTAGGTGGAGATACCATAGATTTGGACACT[C/T,G]
AATGTCTATCTACAATGTTGCATAACATTGAAGACGCAGAGGACAACGACAGAGATTTTGAGAAGTTTAGTAAGTTGGTGGAAGATTGTCAGATGCCCTT
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 | 68.80% | 19.70% | 10.88% | 0.66% | NA |
All Indica | 2759 | 94.20% | 2.50% | 3.37% | 0.00% | NA |
All Japonica | 1512 | 33.50% | 43.70% | 20.77% | 2.05% | NA |
Aus | 269 | 23.00% | 45.40% | 31.60% | 0.00% | NA |
Indica I | 595 | 91.40% | 2.00% | 6.55% | 0.00% | NA |
Indica II | 465 | 96.60% | 0.40% | 3.01% | 0.00% | NA |
Indica III | 913 | 95.00% | 3.90% | 1.10% | 0.00% | NA |
Indica Intermediate | 786 | 93.90% | 2.30% | 3.82% | 0.00% | NA |
Temperate Japonica | 767 | 52.90% | 21.40% | 21.90% | 3.78% | NA |
Tropical Japonica | 504 | 12.90% | 72.00% | 15.08% | 0.00% | NA |
Japonica Intermediate | 241 | 14.50% | 55.60% | 29.05% | 0.83% | NA |
VI/Aromatic | 96 | 21.90% | 62.50% | 15.62% | 0.00% | NA |
Intermediate | 90 | 71.10% | 21.10% | 7.78% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0609473231 | G -> C | LOC_Os06g16510.1 | missense_variant ; p.Gln71Glu; MODERATE | N | Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
vg0609473231 | G -> A | LOC_Os06g16510.1 | stop_gained ; p.Gln71*; HIGH | stop_gained | Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
vg0609473231 | G -> DEL | LOC_Os06g16510.1 | N | frameshift_variant | Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0609473231 | NA | 2.46E-09 | mr1666 | 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 |
vg0609473231 | NA | 3.04E-07 | mr1570_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 |