Single base exon in splice alignment

[baraaorabi]

I have a long read (ONT) that I am aligning to the reference genome using Minimap2 -x splice mode.
Minimap2 is generating a 1bp exon as part of the alignment of this alignment:

$ wget https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz
$ mamba create -n minimap2-test -c bioconda minimap2==2.26
$ mamba activate minimap2-test
(minimap2-test) $ minimap2 -c --eqx -x splice -t 32 Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz  \
  <(echo -e ">read1\nAATGTACTTCGGTTCAATTACGTATTGCTTCAGGTAGTCATTGATGA
CATCATCCACGGGTAATTGCTGAGGGAGAAGCTGGACGCAGTTTAAATGATCCTTATTGGCCATGTGCAATGGAGATAATCCATTGCTGATTTTGAAAGAATGGGGGTGCGAGCTCGATCAAGCAGCATTTCTACCACCTGCTCGTGGCCACATGCTCACAGTGCAGTGAGTGTCAGACCAT
CCTGGTTTTGGCATCGATTTTAGCTCCTCATCGAGCAATAGTTTTACCATATTTGCATTTATCCTTTTTGATGCAACATGTGGAGTTGATGTCATTCCTTGCAGTGAAATCACAGCAGCCATCGGTTTAACAGTCAACGTGGCTACATAGATATTTCCATAGTGAGCAGCTATGTAGGCAGG
TGAAGCCACTCTTTAGATTCCACATCTGCATTTTGTCATTCTGCAGCAGCAAGGCAGCGGCTTCGTGTCGTCCTTTTCGGGCCGCGATCATGAAGAGCTGGGAGACGCACTTTCCTTTGGTGTCATTCACTAGACAGGAGCAGAAACGACTTGGTCGTGACTTCATTGCAAAGCCACTGCCA
ATGGTGTAAGCCATCTCTGTGGCTAGGCTCTGGCTGCCCCATTATCAAGAAACTTGACAACTTCAGTGATTTTCCTGGAGCTGCCATATACAATGGCGTGAAATCATTCGGAGATTGTGCATTGGCATTGGCCTCCCATGTTAGTAACCAAGACTTTACCACCTCTGCGTGCCCAGCCAAAG
ATGCGATGTACCAATGCTGTGTCCTTATCTTTTAGCTGCATCCACATTAGCCTCTCTGCAGCAGCTCAGAAACAACCTCTATGGCCTTCTTTGGAAGAGTGGAGAGCGTTCAACCCATTCTGATTGCAAATGTTGATGTCAACTCCATTTTTTATGTAGGTCAGGAGCTTTTCAAGTTCAGC
TCGAGCTGCTCTTAAGTAGCTTGCATTGCGCATCAGACTTTTTCCTTCCTTTTCCTATGAGCGGGGTTGGATTTTCTCCTTTGGTTCTCCACATCTTTCCCTTTTAAATCCAGGTGAAGTTTACTTAAAGACAGGATCACCGCCGGTATTCCAATCATCCAAAACTGGCAGAGTCAAAGCAT
TGAGACCAAAGTCCATTTACGGGTGCTCCCAGGCAAAGCAGCCACTGCTTAAGCCAGTCCTGCTGTCAGAGAGGCGCGGCTGCTAATGTAGCCCTGTTCAGCTTTCCTCGGAAGAAACGGGGTGTTCCTCTATATCAAGCAGTGAATTATTCTTCTAAAAGAAAATCATATTTAACCTTTCA
TTTTTAACCAATCGTTACCCTGAGATAAGGTCTGACCAGACTTTGTTGCTTGTTCCTCCACGGTGGTTTGAGCCTGAAATGGTGGGAGAGAGAAGAGAGGAACACACACACACACCCTCACACACACAGAAATAAAGCTACAGACTGCAATACGTAACAAGACGAAAGT")

This generates the following PAF alignment:

read1       1490    29      1469    +       10      133797422       60208124        60572958        869     1483    60      NM:i:614        ms:i:645        AS:i:292        nn:i:0  ts:A:-tp:A:P  cm:i:79 s1:i:433        s2:i:171        de:f:0.0833     rl:i:0  cg:Z:14=1X18=1D2=2D5=2X27=2D4=1X1=1D28=5178N1I2=2D1=1X16=2I2=1I14=1X25=3D1=1X4=1D12=1I12=1D21177N29=1D31=3X18=3D4=1I10=27072N6=1X7=1D10=1D1X12=1I14=1X26=1X1=1D2=1X1=1D11=1877N4=1I17=1D19=1X3=1X5=1D10=1I16=1I21=1D18=1X4=1I7=1I19=1X1=2X24=1D7=1D6110N20=1D3=1X5=1X2=3D17=1D2=1D13=1I24=1X4=8544N1=1X14=1X6=1I2=1I4=1I2=1I11=1D14=1X22=1I1X10=2D5=1I1=177N4=1D16=1X2=2D29=2D17=2D1=1D21=389N10=522I111186N1=182183N27=1I14=

Note the 1bp match (111186N, 1=, 182183N). Why is there such a single basepair match? It looks like Minimap2 is trying to force splicing on this read since the total of the two surrounding splice gaps is >200Kbp

[lh3]

That is probably the case, I guess.