#
# Use the accession number of a published genome.
#
#       bash report-variants.sh MT019529
#

# Stop on error
set -uex

# The query
SEQ=$1

# The reference entry
REF=NC_045512

# Perform the data fetch and alignment
bio fetch $REF $SEQ --format fasta | mafft --auto --preservecase --quiet - | bio format --diff