Search for Variation information by Variation ID:
Detailed information for vg0142999481:
| Variant ID: vg0142999481 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999481 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACCCGTCCTGTACCCTCTTGATTATGCAAGATTTGACCGAGGGGGTAAGACGTAACTACTGTGACCCGATGCGCCTGGAAATAATGGCGCAGTTTCCTC[G/A]
AGGCCATTAGAATAGCGTAAAGCATCTTCTGGGCCTGAGGGTATCGGGTTTTGGCGTCCCGGAGGGCCTCACTAACAAAGTAGACGGGCCGCTGCACCTT
Reverse complement sequence
AAGGTGCAGCGGCCCGTCTACTTTGTTAGTGAGGCCCTCCGGGACGCCAAAACCCGATACCCTCAGGCCCAGAAGATGCTTTACGCTATTCTAATGGCCT[C/T]
GAGGAAACTGCGCCATTATTTCCAGGCGCATCGGGTCACAGTAGTTACGTCTTACCCCCTCGGTCAAATCTTGCATAATCAAGAGGGTACAGGACGGGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 15.80% | 0.10% | 8.19% | 75.92% | NA |
| All Indica | 2759 | 10.60% | 0.20% | 9.57% | 79.63% | NA |
| All Japonica | 1512 | 21.40% | 0.10% | 3.70% | 74.87% | NA |
| Aus | 269 | 39.00% | 0.00% | 11.90% | 49.07% | NA |
| Indica I | 595 | 6.10% | 0.00% | 4.37% | 89.58% | NA |
| Indica II | 465 | 4.30% | 0.20% | 5.59% | 89.89% | NA |
| Indica III | 913 | 16.80% | 0.20% | 16.43% | 66.59% | NA |
| Indica Intermediate | 786 | 10.70% | 0.30% | 7.89% | 81.17% | NA |
| Temperate Japonica | 767 | 38.90% | 0.00% | 0.26% | 60.89% | NA |
| Tropical Japonica | 504 | 2.40% | 0.00% | 9.33% | 88.29% | NA |
| Japonica Intermediate | 241 | 5.40% | 0.40% | 2.90% | 91.29% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 27.08% | 67.71% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 10.00% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999481 | G -> A | LOC_Os01g74230.1 | missense_variant ; p.Ser1174Leu; MODERATE | nonsynonymous_codon ; S1174L | Average:7.978; most accessible tissue: Callus, score: 15.971 | benign  |
0.774 |
DELETERIOUS | 0.00 |
| vg0142999481 | G -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:7.978; most accessible tissue: Callus, score: 15.971 | N | N | N | N |