Coccidioides Population Genomics Analysis

Subfolders organized around mapping to a specific reference and species sample set.

1. Dataset
   • C. immitis strains
   • C. posadasii strains
   • all Coccidioides strains
2. Primary Genotyping and Comparison Analyses
   • Variant calling (reads to VCF)
     • C. immitis RS C. immitis only aligned to RS genome
     • C. posadasii str Silveira 2022 C. posadasii only aligned to Silveira (2022 Nanopore genome)
     • [All strains to C. immitis RS](all_C_immitis_RS] - all Coccidioides aligned to RS
     • [All strains to C. immitis WA 211](all_C_immitis_ref_WA211] - all Coccidioides aligned to Washington 211 asm (this Ci. strain does not have evidence of introgressions)
     • [All strains to C. posadasii str Silveira 2022](all_C_posadasii_refSilv2022] - all Coccidioides aligned to Silveira 2022 asm
   • CNV
     • [Ci RS ref CNV_plots](all_C_immitis_ref_RS/results/CNV_plots/]
     • [Ci WA211 ref CNV_plots](all_C_immitis_ref_WA211/results/CNV_plots/]
     • [Cp Silv2022 ref CNV_plots](all_C_posadasii_refSilv2022/results/CNV_plots]
3. Population and Genomewide analyses

• Population Structure, Introgression testing
• Scans for selection and summary statistics
• Identifying outlier genes with high substitution counts
• GWAS tests for association with strain traits
• Drug resistance alleles