unusual alignment rates for IgG and H3K27me3 in cuttag

Question

[david]

I am using Bowtie2 to align my cut&tag data with the reference genome mm10, and the spike-in species is Ecoli. However, I obtained abnormal alignment rates. There is a substantial proportion of H3K27me3 aligning to mm10 with >1 times mapping, while IgG has a very low overall alignment rate. However, when aligned to the spike-in reference genome, the H3K27me3 alignment rate is very high. As follows:

# H3K27me3 aligns to mm10
   22786978 reads; of these:   22786978 (100.00%) were paired; of these
      968606 (4.25%) aligned concordantly 0 times
      14874420 (65.28%) aligned concordantly exactly 1 time
     6943952 (30.47%) aligned concordantly >1 times
  95.75% overall alignment rate

# igg aligns to mm10
 16022333 reads; of these
  16022333 (100.00%) were paired; of these:
    5093628 (31.79%) aligned concordantly 0 times
    6672786 (41.65%) aligned concordantly exactly 1 time
    4255919 (26.56%) aligned concordantly >1 times
68.21% overall alignment rate

# H3K27me3 aligns to spike-in
 22786978 reads; of these:
  22786978 (100.00%) were paired; of these:
    22130710 (97.12%) aligned concordantly 0 times
    656268 (2.88%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
 2.88% overall alignment rate

and my bowtie2 command is:

bowtie2 \
--local \
--end-to-end \
--very-sensitive-local \
--dovetail \
--no-mixed \
--no-unal \
--no-discordant \
--phred33 \
-I 10 \
-X 700 \
-p ${cores} \
-x ${ref} \
-1 ${trimPath}/${name}_1_val_1.fq.gz \
-2 ${trimPath}/${name}_2_val_2.fq.gz 2> ${summary}/${name}.txt | samtools view -bS -F 0x04 -q 10 > ${bamPath}/${name}.bam