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Last column in UCSC cytoBands.txt files

The file for chromosomal banding coordinates provided by UCSC (cytoBands.txt) has 5 columns like so: 

chr1    0   2300000 p36.33  gneg
chr1    2300000 5300000 p36.32  gpos25
chr1    5300000 7100000 p36.31  gneg
chr1    7100000 9200000 p36.23  gpos25
chr1    9200000 12600000    p36.22  gneg

I am not sure what the 5th column means (gneg, gpos25, acen). I assume they correspond to the locations the way 4th column does, just with a different nomenclature? 'acen' seems to be the centromere, but gneg or gpos are used for every other location, including q arms.

Any insight much appreciated!

Edit: Removed link that does not work anymore

ucsc karyotype
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updated by sina.majidian • sina.majidian • written by cookersjs • cookersjs

the link is no longer valid

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written by timing • timing

1 answer

I am not sure what the 5th column means

Giemsa stain results : https://en.wikipedia.org/wiki/Giemsa_stain / https://en.wikipedia.org/wiki/G_banding

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! Seems intuitive enough now, the 'g' threw me off.

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written by cookersjs • cookersjs

I have read the wikipedia page but I am still not sure about some of the annotations in the fifth column. I suppose gneg means Giemsa stain positive and gpos means positive, but I am still unsure the difference between gpos25 and gpos50, gpos75, gpos100. I am also not sure what gvar and stalk refer to. The following is the unique values of the fifth column of hg38 cytoband.txt. 

gneg                
gpos25              
gpos50              
gpos75              
gpos100             
acen                
gvar                
stalk

Thanks!

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written by timing • timing

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