Variant ID: vg0722707172 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 22707172 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCACTCGCGAAGTTAATGGCCGCATCTCACTACGCGTATCAAGTGCTCAAGATGCTGGGACCGAAGGGAACAATCACTATTCAAGGGAATGCTAAGCTGG[T/C]
AGTGCAATGCGACAAGCGGAGCGTCGACATGGTCGAGCACACGCCCAGCCCACCCGACACAGCCGAGCCACCCAAGAAACTGAGCAAAACAAACAAGACG
CGTCTTGTTTGTTTTGCTCAGTTTCTTGGGTGGCTCGGCTGTGTCGGGTGGGCTGGGCGTGTGCTCGACCATGTCGACGCTCCGCTTGTCGCATTGCACT[A/G]
CCAGCTTAGCATTCCCTTGAATAGTGATTGTTCCCTTCGGTCCCAGCATCTTGAGCACTTGATACGCGTAGTGAGATGCGGCCATTAACTTCGCGAGTGC
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 89.50% | 8.40% | 2.09% | 0.00% | NA |
All Indica | 2759 | 89.50% | 9.70% | 0.80% | 0.00% | NA |
All Japonica | 1512 | 93.30% | 1.80% | 4.96% | 0.00% | NA |
Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 83.90% | 14.00% | 2.15% | 0.00% | NA |
Indica III | 913 | 83.40% | 16.10% | 0.55% | 0.00% | NA |
Indica Intermediate | 786 | 92.20% | 6.90% | 0.89% | 0.00% | NA |
Temperate Japonica | 767 | 88.40% | 2.20% | 9.39% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 95.00% | 3.70% | 1.24% | 0.00% | NA |
VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 83.30% | 14.40% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0722707172 | T -> C | LOC_Os07g37860.1 | missense_variant ; p.Val963Ala; MODERATE | nonsynonymous_codon ; V963A | Average:43.893; most accessible tissue: Minghui63 young leaf, score: 59.171 | unknown | unknown | TOLERATED | 1.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0722707172 | NA | 3.81E-10 | 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 |
vg0722707172 | NA | 1.26E-06 | mr1071 | 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 |
vg0722707172 | NA | 9.20E-06 | mr1080 | 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 |
vg0722707172 | NA | 7.36E-06 | mr1203 | 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 |
vg0722707172 | NA | 7.53E-06 | mr1382 | 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 |
vg0722707172 | NA | 1.77E-07 | mr1829 | 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 |
vg0722707172 | 1.27E-08 | 7.47E-14 | mr1829_2 | 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 |
vg0722707172 | NA | 2.93E-06 | 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 |
vg0722707172 | 7.04E-08 | NA | mr1842_2 | 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 |