Thank you for using the UCSC Genome Browser and your question about the hg38 centromere regions.
New to hg38 on our genome-test development site is a centromeres track (bright red track below the Hg19 Diff track, with the table centromeres). This track shows the location of Karen Miga's centromere model sequences. However, these annotations can be smaller than the centromeres shown in the chromosome ideogram and Chromosome Bands track. The hg38.cytoBandIdeo table has rows used to show centromere locations in the chromosome ideograms where each chromosome has two adjacent entries: a p11 (or p11.1) and q11 (or q11.1). For chr9, there are 9p11.1 and 9q11 from chr9:42200000-43000000 and chr9:43000000-45500000 respectively.
A couple things to note in the above session:
1. There are annotations extending into 9p11.1 and 9q11.
2. The Gap track has some tiny gaps in 9q11, close to the centromere (bright red) track-- but notice the large gap labeled "heterochromatin". That's not the centromere, but it's not accessible to current sequencing technologies either.
In summary, depending on your purpose you could use the centromere model regions (red), or the broader Chromosome Bands Ideogram definition of centromere which overlap some annotations (cytoBandIdeo table), or the regions of the assembly that are just NNNNN's (Gap track).
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu
. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu
All the best,
UCSC Genome Bioinformatics Group