Medaka SNP Call Shows Alternative Base Not Visible in IGV Despite Using Correct Model and Guppy Version

[YomnaGohar]

I used Medaka to call variants in my samples and noticed that Medaka called an SNP at a position, assigning an alternative base that is not visible in IGV. Please see the attached PNG as an example. The corresponding VCF entry for this position is:
contig_2 199519 . A T 9.132 PASS DP=12;DPS=4,8 GT:GQ 1:9

my data was sequenced using different naopores but they were all called with guppy version 615. I used medaka model corresponding to the napores with the highest depth so the medaka model used is r1041_e82_400bps_sup_variant_g615
The command used was
medaka_variant -r /gpfs/project/yogah100/ToxoME49_2015_2022/combined_with_pipline_after_rebasecalling_and_herro_using_all_read_that_donot_map_to_human_or_mouse/after_mit_removal/assembly/nano-corr/toxoplasma-gondii-annotation_results/scafs_with_xie_et_apicoblast.fasta.map-ont.mmi -i /gpfs/project/projects/DiltheyLab/projects/Toxoplasma/nanopore_long_reads_fastq/samples_ToxoME49_2000_B/combined_with_pipline_after_rebasecalling/non_mit_reads.fastq -m /gpfs/project/projects/DiltheyLab/projects/Toxoplasma/medaka_models/r1041_e82_400bps_sup_variant_g615_model_pt.tar.gz -t 10 -o medaka -b 50 2> medaka_2000B.log
Logging

medaka_2000B.log

Environment (if you do not have a GPU, write No GPU):

• Installation method pip install
• OS: CentOS Linux 7 (Core)
• medaka version medaka 2.0.1
• GPU model No GPU
• Nvidia driver version
• CUDA version
• cuDNN version

Additional context
Add any other context about the problem here.