Variant ID: vg1203268826 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 3268826 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTTGGACCTCTTTGACAGCCATCACAGCCTTGCCCGTGCGGTCATTTCTGAATTTTCTCCACGTCATGGGAGCTTGACTTGGCCTTGGCGGCTGTCCCTG[A/G]
TTCGCCAGCTGAGGTTGGCGAACGGTGAGAGGAGTCGGTTCGGCGACCTGTGCTTGTACTTGGGCTTGGGCAGTGGCGATGGAGGCTTTATCGTACTCGG
CCGAGTACGATAAAGCCTCCATCGCCACTGCCCAAGCCCAAGTACAAGCACAGGTCGCCGAACCGACTCCTCTCACCGTTCGCCAACCTCAGCTGGCGAA[T/C]
CAGGGACAGCCGCCAAGGCCAAGTCAAGCTCCCATGACGTGGAGAAAATTCAGAAATGACCGCACGGGCAAGGCTGTGATGGCTGTCAAAGAGGTCCAAG
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 35.80% | 13.90% | 8.65% | 41.60% | NA |
All Indica | 2759 | 5.80% | 19.20% | 12.69% | 62.38% | NA |
All Japonica | 1512 | 93.10% | 1.30% | 2.31% | 3.31% | NA |
Aus | 269 | 5.90% | 33.10% | 5.58% | 55.39% | NA |
Indica I | 595 | 4.20% | 7.90% | 6.39% | 81.51% | NA |
Indica II | 465 | 4.70% | 8.60% | 19.78% | 66.88% | NA |
Indica III | 913 | 6.40% | 33.20% | 13.03% | 47.43% | NA |
Indica Intermediate | 786 | 6.90% | 17.70% | 12.85% | 62.60% | NA |
Temperate Japonica | 767 | 95.60% | 0.30% | 3.13% | 1.04% | NA |
Tropical Japonica | 504 | 87.90% | 3.00% | 1.59% | 7.54% | NA |
Japonica Intermediate | 241 | 96.30% | 0.80% | 1.24% | 1.66% | NA |
VI/Aromatic | 96 | 62.50% | 6.20% | 2.08% | 29.17% | NA |
Intermediate | 90 | 55.60% | 16.70% | 7.78% | 20.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1203268826 | A -> DEL | LOC_Os12g06720.1 | N | frameshift_variant | Average:9.281; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
vg1203268826 | A -> G | LOC_Os12g06720.1 | synonymous_variant ; p.Asn615Asn; LOW | synonymous_codon | Average:9.281; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1203268826 | 4.64E-06 | NA | mr1639 | 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 |
vg1203268826 | NA | 3.53E-06 | mr1639 | 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 |