Search for Variation information by Variation ID:
Detailed information for vg0319757598:
| Variant ID: vg0319757598 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757598 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACAGATGAAAACTCGTTCCAGGTGATGGTATGTCCTTCTGGCTGTGATGCTTCGTAGCTATCCCACCACTCTGAAGCCGGTCCAACCAGCTGAGGAGTTG[C/T]
GAAGCCAACCCGCTCCTGGTCGGTGCACTGAATCAACCCTAGCTTCTTCTCGATTGTGCGCAACCAATCACTGGCTTCCATAGGATCGACGGCAATGGCA
Reverse complement sequence
TGCCATTGCCGTCGATCCTATGGAAGCCAGTGATTGGTTGCGCACAATCGAGAAGAAGCTAGGGTTGATTCAGTGCACCGACCAGGAGCGGGTTGGCTTC[G/A]
CAACTCCTCAGCTGGTTGGACCGGCTTCAGAGTGGTGGGATAGCTACGAAGCATCACAGCCAGAAGGACATACCATCACCTGGAACGAGTTTTCATCTGT
Allele Frequencies:
| 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 | 30.50% | 1.40% | 17.69% | 50.38% | NA |
| All Indica | 2759 | 3.20% | 0.10% | 26.10% | 70.57% | NA |
| All Japonica | 1512 | 84.10% | 0.10% | 3.31% | 12.57% | NA |
| Aus | 269 | 9.70% | 0.40% | 13.75% | 76.21% | NA |
| Indica I | 595 | 3.50% | 0.00% | 15.46% | 81.01% | NA |
| Indica II | 465 | 4.70% | 0.00% | 23.01% | 72.26% | NA |
| Indica III | 913 | 1.90% | 0.30% | 34.28% | 63.53% | NA |
| Indica Intermediate | 786 | 3.60% | 0.10% | 26.46% | 69.85% | NA |
| Temperate Japonica | 767 | 95.00% | 0.00% | 0.26% | 4.69% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 8.13% | 25.40% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.40% | 2.90% | 10.79% | NA |
| VI/Aromatic | 96 | 18.80% | 55.20% | 8.33% | 17.71% | NA |
| Intermediate | 90 | 44.40% | 7.80% | 23.33% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757598 | C -> T | LOC_Os03g35670.1 | missense_variant ; p.Ala476Thr; MODERATE | nonsynonymous_codon ; A476T | Average:6.217; most accessible tissue: Minghui63 flower, score: 10.335 | possibly damaging  |
1.571 |
DELETERIOUS | 0.02 |
| vg0319757598 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:6.217; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |