Genomic Codon Composition and Epidemiological Landscape of H5N9 Influenza A Virus

This dataset comprises 439 complete H5N9 influenza A virus sequences from NCBI, processed using local Python and Biopython scripts.
Sequences underwent completeness validation, MAFFT alignment (--auto), and trimming. Per-sequence metrics include ENc, CAI (human/avian), GC3, RSCU, CPB, and PR2.
Collection year and country were extracted from FASTA headers. Includes aligned FASTA, codon metrics CSV, QC reports, and plots.
ODON USAGE SUMMARY: H5N9
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Total sequences: 439
Valid CDS: 96 (21.9%)
Valid CAI: 96 (21.9%)

METRIC STATISTICS (Mean ± SD):
ENc (Effective Number of Codons): 34.265 ± 2.156
CPB (Codon Pair Bias): 5.206 ± 1.119
CAI_human: 3.419 ± 0.156
CAI_avian: 3.440 ± 0.159
GC3: 0.453 ± 0.030
PR2_A (A3/(A3+T3)): 0.586 ± 0.031
PR2_G (G3/(G3+C3)): 0.508 ± 0.048

INTERPRETATION:
→ Strong codon usage bias (ENc < 40)
→ Similar adaptation to human/avian hosts
Data processed by [e-mail]