Variant ID: vg0100975309 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 975309 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACTTTTGGGTCCTCACTCGCTCTGGGAAATGGAAACCTTGCCTTGACCGGGTTAAACGAACCGCCTCCGGCTGTGAAGAGAGGCTAAACAGCCTCTCAT[C/A]
ATCATGATGTGACAGGGGATGTCAGGCGGCACACCGCCTGACATGCAACCAGTGTGCAGGCGCACTACCCTGGTCACGTCAGTCATTCGACCGGTCGCAG
CTGCGACCGGTCGAATGACTGACGTGACCAGGGTAGTGCGCCTGCACACTGGTTGCATGTCAGGCGGTGTGCCGCCTGACATCCCCTGTCACATCATGAT[G/T]
ATGAGAGGCTGTTTAGCCTCTCTTCACAGCCGGAGGCGGTTCGTTTAACCCGGTCAAGGCAAGGTTTCCATTTCCCAGAGCGAGTGAGGACCCAAAAGTC
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 35.00% | 7.90% | 2.20% | 54.91% | NA |
All Indica | 2759 | 24.20% | 0.80% | 1.85% | 73.07% | NA |
All Japonica | 1512 | 50.70% | 18.40% | 0.53% | 30.36% | NA |
Aus | 269 | 56.90% | 0.00% | 16.36% | 26.77% | NA |
Indica I | 595 | 12.90% | 0.20% | 1.51% | 85.38% | NA |
Indica II | 465 | 7.10% | 2.40% | 2.58% | 87.96% | NA |
Indica III | 913 | 36.10% | 0.20% | 1.75% | 61.88% | NA |
Indica Intermediate | 786 | 29.10% | 1.10% | 1.78% | 67.94% | NA |
Temperate Japonica | 767 | 70.50% | 23.10% | 0.26% | 6.13% | NA |
Tropical Japonica | 504 | 14.30% | 8.70% | 1.19% | 75.79% | NA |
Japonica Intermediate | 241 | 63.90% | 23.70% | 0.00% | 12.45% | NA |
VI/Aromatic | 96 | 29.20% | 63.50% | 1.04% | 6.25% | NA |
Intermediate | 90 | 40.00% | 13.30% | 0.00% | 46.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0100975309 | C -> A | LOC_Os01g02780.1 | upstream_gene_variant ; 1982.0bp to feature; MODIFIER | silent_mutation | Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
vg0100975309 | C -> A | LOC_Os01g02790.1 | upstream_gene_variant ; 1457.0bp to feature; MODIFIER | silent_mutation | Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
vg0100975309 | C -> A | LOC_Os01g02780-LOC_Os01g02790 | intergenic_region ; MODIFIER | silent_mutation | Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
vg0100975309 | C -> DEL | N | N | silent_mutation | Average:31.614; most accessible tissue: Minghui63 young leaf, score: 65.161 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0100975309 | 1.66E-07 | NA | Grain_weight | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |