Hello,
We noticed a difference between the MPC v4.1.1 preprint and the downloadable score file.
The preprint (https://doi.org/10.1101/2024.04.11.588920), Methods > Transcripts, states:
“For high quality transcripts, we excluded transcripts that had outlier variant counts: zero expected or too many observed pLoF, missense, or synonymous variants; or too few observed synonymous variants. This totaled 17,841 transcripts, 96% from MANE Select and 4% canonical. We also make MCR and MPC information available for the 1,534 transcripts with outlier counts, but caution that scores may be less accurate in these sequences.”
That’s 19,375 transcripts total. But counting the unique transcript IDs directly in the downloadable score file (gs://gcp-public-data–gnomad/papers/2026-rmc/gnomad_v4.1.1_mpc.tsv.bgz) with:
zcat gnomad_v4.1.1_mpc.tsv.gz | tail -n +2 | cut -f3 | sort -u | wc -l
gives 18,245 unique transcripts, not 19,375.
Can you clarify why these counts differ?