What does '|' mean in the multiple sequence alignment?

[mengyao]

In the 'alignments' folder A_gen.txt file, there are several lines contain " | " symbol, for example:
A_01:01:01:01 G | ATGGCCGTC ATGGCGCCCC GAACCCTCCT CCTGCTACTC TCGGGGGCCC TGGCCCTGAC CCAGACCTGG GCGG | GTGAGT GCGGGGTCGG GAGGGAAACC
A_01:01:01:02N - | --------- ---------- ---------- ---------- ---------- ---------- ---------- ---- | ------ ---------- ----------
A*01:01:01:03 * | --------- ---------- ---------- ---------- ---------- ---------- ---------- ---- | ------ ---------- ----------

May I ask what do these " | " symbols mean?

Many thanks,

Mengyao

[ANHIG]

Many thanks for your query, a Readme file has been added to this directory.

[mengyao]

Hi,

Thank you very much for your quick help.

Yours,

Mengyao

On Jun 9, 2016, at 4:51 AM, Anthony Nolan HLA Informatics Group notifications@github.com wrote:

Many thanks for your query, a Readme file has been added to this directory.

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[mengyao]

Hi,

May I ask you two other questions?

In the README file, it states “The entry for each allele is displayed in respect to the reference sequences.”

1. In the gDNA alignment file, is the 1st haplotype for example “DQA1*01:01:01:01” the same as the reference sequence?
2. Which version of the human genome reference does the alignment correspond to?
3. What’s the relationship between the coordinates labeled on the alignment and the human reference coordinate?

Many thanks,

Mengyao

On Jun 9, 2016, at 4:51 AM, Anthony Nolan HLA Informatics Group notifications@github.com wrote:

Many thanks for your query, a Readme file has been added to this directory.

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You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub #63 (comment), or mute the thread https://github.com/notifications/unsubscribe/AAlVdPra60rjz_9yTuyy9BJ9-F9gw5mkks5qJ9QcgaJpZM4IxQcR.