Missing gaps elements in mm9

[Ricardo A. Verdugo]

Dear UCSC staff:

I often use your Gap tables for plotting chromosomes. However, I have a
problem when using the mm8 and mm9 genomes. Most elements are missing
from that table. I am particularly interested in telomeres. Since they
are missing, the chromosomes in the "Gap" table are shorter than in they
should be.

Here I show counts of elements of the "type" column of the Gap tables of
three genome assemblies obtained from the Table Browser of UCSC:

> table(mm8_gap$Name)

centromere contig fragment
21 169 1218

> table(mm9_gaps$Name)

centromere contig fragment
21 281 709

> table(mm10_gap$Name)

centromere clone contig fragment other short_arm telomere
20 114 104 1 384 21 42

Should I look somewhere else or this information cannot be obtained for
mm8 and mm9?

Thank you

Ricardo Verdugo

[Christopher Lee]

Hi Ricardo,

Thank you for your question about missing telomere elements in the mm8 and mm9 gap tables.
Our gap tables only contain data from the NCBI public build, and thus if mm8 and mm9 have
no information about telomeres in their gap tables, it is because NCBI did not annotate it
in their release.

We recommend using the mm10 data as it is the most recent mouse assembly released, and
thus contains the most up to date and accurate information.

You may also try contacting the NCBI help desk, https://www.ncbi.nlm.nih.gov/home/about/contact.shtml,
about updating this information on their site.

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.

Ricardo Verdugo

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