New estimate for the number of new mutations in each human genome

I originally tried to post this 5/4
https://www.nature.com/articles/s41586-025-08922-2
The article is open access.
They sequenced a 4 generation pedigree and claimed to have assembled around 95% of the human genome for each individual.
They found around 150 de novo mutations (DNM) average.  74.5 single nucleotide variants (SNP, single nucleotide polymorphisms).  7.4 indels not involved with tandem repeats and 65.3 indels associated with tandem repeats (this is consistent with previous work indicating an equal number of indels as SNPs).  The abstract doesn't indicate the number of inversions and translocations detected, but it is difficult to detect inversions and translocations with short read tech.  They claim to have used HiFi and long read technology.  They also claim to have resolved recombination sites and did not identify increased structural variation involved in recombination junctions.  They may have an under estimate for tandem repeat changes.  Microsatellites are estimated to have a 10^-5 mutation rate, and I've worked with a large tandem duplication (180 kb) that has a rate of change due to recombination of around 1 in 1,000.  The larger the tandem (dinucleotide repeats have the fastest rate of change) the more stable the repeat is until you get to lengths where aberrant pairing between repeats and subsequent recombination become an issue.
This is significantly higher than the previous accepted estimate, but is lower than the first estimate that I recall of around 200 mutations per genome.  Their range was 98-206 DNM per genome.
A much larger data set is likely needed to get the actual rate because we know that there are a lot of places in the genome with very high mutation rates.  The single nucleotide mutation for achondroplastic dwarfism occurs at around 1 in 14,000 live births and is detected because it is a dominant mutation, and there are other loci that mutate at a faster rate.  You have to analyze enough pedigrees to get a more accurate understanding of how the high mutation rate sites are affecting the mutation rate.  The wide range in mutations detected indicates that there may be a significant number of rapidly mutating sites.
Ron Okimoto