Identified intermediate variants files for calling de-novo mutations in Colorado potato beetle.

Direct germline mutation rate estimates are scarce in insects, with none available for beetles (Coleoptera), the most speciose order including major pests. We sequenced genomes from 16 trios of Colorado potato beetle (Leptinotarsa decemlineata, CPB)—a pest evolving resistance to many insecticides. We sequenced the genomes of 16 trios derived from two familes and detected 69 de novo SNP mutations that affects a single site in a single offspring. This yields an estimated germline mutation rate of 5.2 × 10-9 (95%CI: 4.0 × 10-9, 6.6 × 10-9) per site per generation, exceeding 1.6-fold of median mutation rates in other insects. The spectrum shows a transition ratio (Ts/Tv = 1.56) that is consistent with other insects.
The files in the folders:
Unique variants identified from GATK pipeline: Chr_all.flt.pass.AC1.vcf.gz
Unique variants identified from MPILEIUP pipeline: joint.chr1-18.flt.AC1.vcf.gz
Concensus variants: CPB-MA.concensus.vcf
The concensus variants were then used for identifying de novo mutations based on trio pedigree information.
Raw data from Sanger-sequencing: SangerSequences.zip