Bowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is Part Of Different Indexes

I am using bowtie2 to map my PE reads.

I have indexed multiple bacterial genomes by putting them together in a multi-fasta file fashion.

bowtie2 -q -a -p 1 -x Multi -1 R100_1.fq -2 R100_2.fq -U 100_Orph.fastq -S 100.sam
samtools view -b -S 100.sam -o 100.bam
coverageBed -abam 100.bam -b BED_RefSeq >>100.cvg
CoverageBed ouput for genome("307679329")is :  307679329       1       25751   72      3568    25750   0.1385631

but when I index genome ("307679329") separately then CoverageBed output is:

307679329       1       25751   449     8369    25750   0.3250097

Can someone explain this differnece