Search for Variation information by Variation ID:
Detailed information for vg0714370352:
| Variant ID: vg0714370352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14370352 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAAGCAATCAAAGCAACCATAAAACCAAGAAAAGAAAAATCACCGGTTGCCGAGGAGAGCCTGGAGGTGGACGATGAGCTTCTCCTCCTGCTCAGTGAAG[T/C]
TCCCCCGCTTGATCCCCGGCTGGAGGTAGTTCGTCCACCGGAGCGGGCAGCTCTTGCTGCAACGCATCACCCCTGCACACACGCACAGATCAAACATGCA
Reverse complement sequence
TGCATGTTTGATCTGTGCGTGTGTGCAGGGGTGATGCGTTGCAGCAAGAGCTGCCCGCTCCGGTGGACGAACTACCTCCAGCCGGGGATCAAGCGGGGGA[A/G]
CTTCACTGAGCAGGAGGAGAAGCTCATCGTCCACCTCCAGGCTCTCCTCGGCAACCGGTGATTTTTCTTTTCTTGGTTTTATGGTTGCTTTGATTGCTTT
Allele Frequencies:
| 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 | 45.20% | 30.70% | 5.86% | 18.24% | NA |
| All Indica | 2759 | 23.80% | 47.40% | 8.99% | 19.79% | NA |
| All Japonica | 1512 | 84.00% | 3.20% | 0.40% | 12.37% | NA |
| Aus | 269 | 26.80% | 24.50% | 7.06% | 41.64% | NA |
| Indica I | 595 | 42.20% | 34.30% | 5.38% | 18.15% | NA |
| Indica II | 465 | 40.20% | 43.20% | 10.11% | 6.45% | NA |
| Indica III | 913 | 3.10% | 61.00% | 7.45% | 28.48% | NA |
| Indica Intermediate | 786 | 24.30% | 44.00% | 12.85% | 18.83% | NA |
| Temperate Japonica | 767 | 86.30% | 0.10% | 0.52% | 13.04% | NA |
| Tropical Japonica | 504 | 92.50% | 4.00% | 0.00% | 3.57% | NA |
| Japonica Intermediate | 241 | 58.90% | 11.60% | 0.83% | 28.63% | NA |
| VI/Aromatic | 96 | 83.30% | 7.30% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 64.40% | 22.20% | 3.33% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714370352 | T -> DEL | LOC_Os07g25150.1 | N | frameshift_variant | Average:16.011; most accessible tissue: Zhenshan97 flower, score: 30.815 | N | N | N | N |
| vg0714370352 | T -> C | LOC_Os07g25150.1 | missense_variant ; p.Asn46Ser; MODERATE | nonsynonymous_codon | Average:16.011; most accessible tissue: Zhenshan97 flower, score: 30.815 | benign  |
0.619 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714370352 | NA | 8.16E-09 | mr1047 | 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 |
| vg0714370352 | NA | 4.35E-06 | mr1189 | 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 |
| vg0714370352 | NA | 1.84E-07 | mr1796 | 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 |
| vg0714370352 | NA | 3.77E-07 | mr1990 | 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 |
| vg0714370352 | 4.97E-06 | NA | mr1226_2 | Ind_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 |