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Detailed information for vg0334133761:
| Variant ID: vg0334133761 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34133761 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 386. )
Flanking Sequence (100 bp) in Reference Genome:
AGGTGTCCCCGTGTGGGACGAGGACAAACAGGAGGAGTTTAACCTACGAGCGCTGCTGTTCGTAACCATCAACGATTGGCCTGCACTTAGCAACCTATCC[G/A]
GACAGTCCAACAAGGGGTACAAGGCTTGCACTCACTGTATGGATGAAACAGAAAGTATGTATCTTAAGCACTGTAGGAAGGTTGTATACATGGGTCATCG
Reverse complement sequence
CGATGACCCATGTATACAACCTTCCTACAGTGCTTAAGATACATACTTTCTGTTTCATCCATACAGTGAGTGCAAGCCTTGTACCCCTTGTTGGACTGTC[C/T]
GGATAGGTTGCTAAGTGCAGGCCAATCGTTGATGGTTACGAACAGCAGCGCTCGTAGGTTAAACTCCTCCTGTTTGTCCTCGTCCCACACGGGGACACCT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.10% | 0.10% | 15.32% | 67.44% | NA |
| All Indica | 2759 | 27.50% | 0.10% | 16.89% | 55.45% | NA |
| All Japonica | 1512 | 0.70% | 0.10% | 14.15% | 85.12% | NA |
| Aus | 269 | 9.70% | 0.40% | 8.92% | 81.04% | NA |
| Indica I | 595 | 8.40% | 0.00% | 8.74% | 82.86% | NA |
| Indica II | 465 | 32.00% | 0.00% | 16.56% | 51.40% | NA |
| Indica III | 913 | 39.50% | 0.40% | 19.93% | 40.09% | NA |
| Indica Intermediate | 786 | 25.30% | 0.00% | 19.72% | 54.96% | NA |
| Temperate Japonica | 767 | 0.70% | 0.00% | 3.78% | 95.57% | NA |
| Tropical Japonica | 504 | 0.40% | 0.20% | 30.56% | 68.85% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 12.86% | 85.89% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 5.21% | 92.71% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 16.67% | 70.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334133761 | G -> A | LOC_Os03g60010.1 | missense_variant ; p.Gly444Arg; MODERATE | nonsynonymous_codon ; G444R | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.195 |
DELETERIOUS | 0.02 |
| vg0334133761 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |