Search for Variation information by Variation ID:
Detailed information for vg0707517323:
| Variant ID: vg0707517323 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7517323 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
TTAGTTGAGATTAATTGGCCAAACAGTTATTTAACTAAAATTGAGCAAAGTTGAAGACTTACTTGAGGGACAACATCTGGAAAGTGGTCTGTCATGTACA[G/T]
TGAAGCTGGTTGGTGGAATAAATGCAGTTTCCATTCACCCCACCACCTGTCAAAGTTTTTGCTTCTGAATGTTGCCAGTTCTATGTTGTCAATACTACCC
Reverse complement sequence
GGGTAGTATTGACAACATAGAACTGGCAACATTCAGAAGCAAAAACTTTGACAGGTGGTGGGGTGAATGGAAACTGCATTTATTCCACCAACCAGCTTCA[C/A]
TGTACATGACAGACCACTTTCCAGATGTTGTCCCTCAAGTAAGTCTTCAACTTTGCTCAATTTTAGTTAAATAACTGTTTGGCCAATTAATCTCAACTAA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 84.10% | 15.90% | 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 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 78.60% | 21.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 55.60% | 44.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707517323 | G -> T | LOC_Os07g13130.1 | missense_variant ; p.Leu374Met; MODERATE | nonsynonymous_codon ; L374M | Average:43.161; most accessible tissue: Minghui63 panicle, score: 66.554 | benign  |
-0.482 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707517323 | 7.35E-06 | NA | Grain_width | 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 |
| vg0707517323 | NA | 2.67E-06 | mr1064_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 |