Supplemental File 1
module load SRA-Toolkit/3.0.1-centos_linux64
module load Bowtie2/2.5.2-GCC-11.3.0
module load SAMtools/1.16.1-GCC-11.3.0
#Bossier
fasterq-dump --split-files SRR14424420 --outdir $DATADIR #import illumina reads from NCBI
bowtie2 --threads 20 -x ${DATADIR}/Wm82 -1 ${DATADIR}/SRR14424420_1.fastq -2 ${DATADIR}/SRR14424420_2.fastq | samtools sort --threads 20 -o ${DATADIR}/Bossier.bam #map reads to Wm82 reference
samtools index -@ 20 ${DATADIR}/Bossier.bam #index BAM file
samtools consensus -@ 20 -aA -f fasta -r 'Gm10:1415000-1567000' -o ${OUTDIR}/Bossier.fasta ${DATADIR}/Bossier.bam #extract candidate region sequence
#Essex
fasterq-dump --split-files SRR12191283 --outdir $DATADIR #import illumina reads from NCBI
bowtie2 --threads 20 -x ${DATADIR}/Wm82 -1 ${DATADIR}/SRR12191283_1.fastq -2 ${DATADIR}/SRR12191283_2.fastq | samtools sort --threads 20 -o ${DATADIR}/Essex.bam #map reads to Wm82 reference
samtools index -@ 20 ${DATADIR}/Essex.bam #index BAM file
samtools consensus -@ 20 -aA -f fasta -r 'Gm10:1415000-1567000' -o ${OUTDIR}/Bossier.fasta ${DATADIR}/Bossier.bam #extract candidate region sequence
#Forrest
fasterq-dump --split-files SRR19134685 --outdir $DATADIR #import illumina reads from NCBI
bowtie2 --threads 20 -x ${DATADIR}/Wm82 -1 ${DATADIR}/SRR19134685_1.fastq -2 ${DATADIR}/SRR19134685_2.fastq | samtools sort --threads 20 -o ${DATADIR}/Forrest.bam #map reads to Wm82 reference
samtools index -@ 20 ${DATADIR}/Forrest.bam #index BAM file
samtools consensus -@ 20 -aA -f fasta -r 'Gm10:1415000-1567000' -o ${OUTDIR}/Forrest.fasta ${DATADIR}/Forrest.bam #extract candidate region sequence
#PI 96354
fasterq-dump --split-files SRR9714646 --outdir $DATADIR #import illumina reads from NCBI
bowtie2 --threads 20 -x ${DATADIR}/Wm82 -1 ${DATADIR}/SRR9714646_1.fastq -2 ${DATADIR}/SRR9714646_2.fastq | samtools sort --threads 20 -o ${DATADIR}/PI96354.bam #map reads to Wm82 reference
samtools index -@ 20 ${DATADIR}/PI96354.bam #index BAM file
samtools consensus -@ 20 -aA -f fasta -r 'Gm10:1415000-1567000' -o ${OUTDIR}/PI96354.fasta ${DATADIR}/PI96354.bam #extract candidate region sequence