Is there a way to tell which chromosome a gene is on, by looking at the "Chromosome/scaffold name"

Question

I recently got a data set, from which I need to figure out which chromosome a gene is from, but the head of the data reads like:

Gene ID Description     Gene type       Gene End (bp)   Gene Start (bp) Strand  Associated Gene Name    Chromosome/scaffold name

while one entry of the data is like:

ENSG00000252303 RNA, U6 small nuclear 280, pseudogene [Source:HGNC Symbol;Acc:HGNC:47243]       snRNA   67546754        67546651        1       RNU6-280P       CHR_HG2128_PATCH

It looks like the last column is the information about which chromosome the gene comes from, but how to interpret the "CHR_HG2128_PATCH"?

Answer 1

What you are looking at is a patch, not an actual chromosome location. HG-2128 is an issue ID, something that the Genome Reference Consortium uses to track issue with references. Information regarding that specific patch is here. The issue is described as a "Possible misassembly or indel variation in GRCh38 within AL049860.8."

During the alignment step before you received your data, someone used a top level assembly version of the reference genome. This includes extra, accessioned scaffolds tacked on to the end of the file that contain the fix. These scaffolds represent what will be found in the next major release of the genome. The fixes aren't applied directly to the reference as soon as they are found due to the inevitable disruption of coordinates. So reads mapped to this FIX patch rather than the primary original scaffold in the primary assembly, on which the RNU6-280P gene resides.

The coordinates are slightly different. In the current GRCh38.p12 assembly the RNU6-280P gene is located at chr6:67546651-67546754 (source). You can see that the coordinates are very close to those indicated in the table you provided (Gene Start, Gene End) but are indeed different.

Here is some more information on patches.