Variant ID: vg0722812632 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 22812632 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGGACCCACATGTCAGTTTCACACACAAATTAATAAAAAATGACGGGGCCCACGTGGGCCCCACATGTCATTTCACCCCTCTTCTTCCTCCTCTCTCTC[C/T]
CCATCTCCCATCTCTTCATCTCTCTCCCCTTTCCTCTCTCGCTTCGGTGCTCGCCCCGCTCTCCTCGTCCCCAGGCCTCTCCGACCGCCTCCTCGCCGCC
GGCGGCGAGGAGGCGGTCGGAGAGGCCTGGGGACGAGGAGAGCGGGGCGAGCACCGAAGCGAGAGAGGAAAGGGGAGAGAGATGAAGAGATGGGAGATGG[G/A]
GAGAGAGAGGAGGAAGAAGAGGGGTGAAATGACATGTGGGGCCCACGTGGGCCCCGTCATTTTTTATTAATTTGTGTGTGAAACTGACATGTGGGTCCCA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0722812632 | C -> T | LOC_Os07g38050.1 | upstream_gene_variant ; 2762.0bp to feature; MODIFIER | silent_mutation | Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
vg0722812632 | C -> T | LOC_Os07g38030.1 | downstream_gene_variant ; 3248.0bp to feature; MODIFIER | silent_mutation | Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
vg0722812632 | C -> T | LOC_Os07g38040.1 | downstream_gene_variant ; 651.0bp to feature; MODIFIER | silent_mutation | Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
vg0722812632 | C -> T | LOC_Os07g38060.1 | downstream_gene_variant ; 4546.0bp to feature; MODIFIER | silent_mutation | Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
vg0722812632 | C -> T | LOC_Os07g38040-LOC_Os07g38050 | intergenic_region ; MODIFIER | silent_mutation | Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0722812632 | NA | 7.56E-09 | Awn_length | Jap_All | Not | 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 |
vg0722812632 | 1.07E-06 | 6.15E-07 | mr1758_2 | 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 |
vg0722812632 | NA | 1.14E-08 | mr1829_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 |
vg0722812632 | NA | 8.66E-07 | mr1842_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 |