What does it mean when the ident values are lower than the query cover?

Question

[Gina]

Hi,

What does it mean when the ident values are lower than the query cover?

[h.mon]

Please put some effort into detailing your question, and providing an example. Why you are puzzled by the identity values being lower than the query coverage?

Please also read How To Ask Good Questions On Technical And Scientific Forums .

Answer 1

[i.sudbery]

Short anwer: Ident is calculated as the % of characters within the covered part of the query that are identical. Thus if your query cover is 90% and your ident is 80%, it means that 80% of the 90% of your query that is covered is identifcal.

Long answer: I'm guesing you are talking about BLAST output.

When BLAST aligns two sequences, it does what is called a local alignment. This means that not all of your query is aligned to the subject. For example, blast might decide that only the first half of your query aligns to a particular subject, while the second half has literally nothing to do with the subject. Thus each alignment has a start and a stop position on the query.

E.g. if we have a 100bp query blast might decide that characters 1 to 50 of the query align to positions 150-200 of some subject, but that characters 51-100 do not.

                             150                            200
                              |                              |
Subject     -----------------------------------------------------------------------
Query                         ||||||||||||||||||||||||||||||||   
                              --------------------------------
                              0                               \
                                                                -------------------------------
                                                               50                             100

Here the query coverage would be 50%, and the Ident is 100% over that alignment.

Now the part of the query that matches, might not match 100%, but the query coverage would still be 50%:

                             150                            200
                              |                              |
Subject     -----------------------------------------------------------------------
Query                         ||||||    ||||||| ||| ||| ||||||   
                              --------------------------------
                              0                               \
                                                                -------------------------------
                                                               50                             100

Here the query coverage is still 50%, but the ident is less than 100%.

Now consider the following

                             150                            200
                              |                              |
Subject     ----------------------------------------------------------------------------------------
Query                         ||||||    ||||||| ||| ||| ||||||   |  |||| ||||  | ||||||
                              ---------------------------------------------------------
                              0                                                    100

In this example, the coverage is 100% (because the alignment starts at the start of the query, and ends at the end), but the ident is less than 100% as not all the positions align.

Part of the art of interpreting a BLAST result is choosing between high ident matches across short stretches and low ident matches across long stretches.

Answer 2

[n,n]

In BLAST ident percentage is the extent to which two aligned sequences have the same exact nucleotides or aminoacids in the same positions, so for short how similar they are qualitatively. Query cover on the other hand is more of a "quantitative" thing, since it expresses how much of your query sequence overlaps with a reference; this means the percentage of the query that aligned successfully against the reference.

Now in an alignment the query can align well against the reference but NOT have the same nucleotides or aminoacids in all the positions of that alignment (because of gaps and other residue variation phenomena) so getting more query cover than indent simply means that your sequences align successfully but they aren't as similar in terms of having the same residues (since you didn't give any values its hard to make assumptions btw).

Hope this helps.