I am trying to perform standard qunatification by salmon, using its default quasi-mapping mode. The index was built on the latest GENCODE:

salmon index -t gencode.v29.transcripts.fa.gz -i gencode_transcriptome_index_salmon

Then I run mapping:

salmon quant -i gencode_transcriptome_index_salmon -l SF -r mate1.fq.gz -o quant1 --writeUnmappedNames --validateMappings

(in reality I have paired-end readings, but for simplified example I show as a stranded single-end). In the output, I get >30% unmapped reads. After manual BLAST, it seems that most abundant of them actually belong to ENST00000316193.12 - transcript that looks quite ordinary, is present in the gencode, etc. From the 150nt of the read, there's just a single mismatch, with all others being a perfect match - so I really don't understand why it is unmapped. Below is a piece of the actual source fastq file with such "unmappable" reads, and then alignment from manual BLAST:

@A00261:111:HFJ5KDSXX:3:1101:28700:5259 1:N:0:AACAACCA+GGTGCGAA
CCCCGAACCACTCAGGGTCCTGTGGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGCCGTCCAAACCGTTCCGTTATCCAGGCTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00261:111:HFJ5KDSXX:3:1102:25473:13667 1:N:0:AACAACCA+GGTGCGAA
GGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGCCGTCCAAACCGTTCCGTTATCCAGGCTTTTTGACCACGCTATGCTCCAAGCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFF,FFFFFFFFFFFF

_

Query  1    CCCCGAACCACTCAGGGTCCTGTGGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGC  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  108  CCCCGAACCACTCAGGGTCCTGTGGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGC  227

Query  121  CGTCCAAACCGTTCCGTTATCCAGGCTTTT  150
            ||||||||||||||| ||||||||||||||
Sbjct  228  CGTCCAAACCGTTCCCTTATCCAGGCTTTT  257

_

Query  1    GGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGCCGTCCAAACCGTTCCGTTATCCA  120
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Sbjct  131  GGACAGCTCACCTAGTGGCAATGGCTCCAGGCTCCCGGACGTCCCTGCTCCTGGCTTTTGCCCTGCTCTGCCTGCCCTGGCTTCAAGAGGCTGGTGCCGTCCAAACCGTTCCCTTATCCA  250

Query  121  GGCTTTTTGACCACGCTATGCTCCAAGCCC  150
            ||||||||||||||||||||||||||||||
Sbjct  251  GGCTTTTTGACCACGCTATGCTCCAAGCCC  280

I would be grateful if someone could explain what happens here and why such reads cannot be mapped.