genome fasta files as indicated in the samples.txt mapped to mm39 with minimap2 and sequence construction with angsd

mm39: GRCm39.primary_assembly.genome.fa
minimap2: minimap2-2.26_x64-linux
samtools: 1.19-3-g62195d3 (using htslib 1.19-4-gb63c363e)
angsd: 0.941-21-g8a58e17 (htslib: 1.19-4-gb63c363e)

example mapping command:
minimap2 -t 12 --sam-hit-only --secondary=no -ax asm5 $REFERENCE $GENOME -R @RG\\tID:WSBg\\tSM:WSBg\\tLB:lib1\\tPL:illumina\\tPU:unit1 | samtools view -b - > $GENOME".asm5.bam"
samtools sort -@ 12 $GENOME".asm5.bam" > $GENOME".asm5.bam.sorted"

minimap2 -t 12 --sam-hit-only --secondary=no -ax asm10 $REFERENCE $GENOME -R @RG\\tID:WSBg\\tSM:WSBg\\tLB:lib1\\tPL:illumina\\tPU:unit1 | samtools view -b - > $GENOME".asm5.bam"
samtools sort -@ 12 $GENOME".asm5.bam" > $GENOME".asm10.bam.sorted"

minimap2 -t 12 --sam-hit-only --secondary=no -ax asm20 $REFERENCE $GENOME -R @RG\\tID:WSBg\\tSM:WSBg\\tLB:lib1\\tPL:illumina\\tPU:unit1 | samtools view -b - > $GENOME".asm5.bam"
samtools sort -@ 12 $GENOME".asm5.bam" > $GENOME".asm20.bam.sorted"

angsd -doFasta 2 -doCounts 1 -maxDepth 99999 -minQ 0 -minMapQ 0 -minInd 1 -setMinDepthInd 1 -setMinDepth 1 -setMaxDepthInd 5 -setMaxDepth 5 -i $GENOME.asm5.bam.sorted -out $GENOME.asm5 -doCheck 0

angsd -doFasta 2 -doCounts 1 -maxDepth 99999 -minQ 0 -minMapQ 0 -minInd 1 -setMinDepthInd 1 -setMinDepth 1 -setMaxDepthInd 5 -setMaxDepth 5 -i $GENOME.asm10.bam.sorted -out $GENOME.asm10 -doCheck 0

angsd -doFasta 2 -doCounts 1 -maxDepth 99999 -minQ 0 -minMapQ 0 -minInd 1 -setMinDepthInd 1 -setMinDepth 1 -setMaxDepthInd 5 -setMaxDepth 5 -i $GENOME.asm20.bam.sorted -out $GENOME.asm20 -doCheck 0