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docs: update images for special classifications.
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CHEWBBACA/docs/user/modules/AlleleCall.rst

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@@ -274,9 +274,9 @@ The column headers stand for:
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genome fragmentation resulting in a shorter CDS prediction by Prodigal. To avoid locus
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misclassification, loci in such situations are classified as *PLOT*.
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.. image:: http://i.imgur.com/41oONeS.png
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:width: 700px
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:align: center
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.. image:: /_static/images/PLOT5_PLOT3_LOTSC.png
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:width: 1400px
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:align: center
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- *LOTSC* - A locus is classified as *LOTSC* when the contig of the query genome is smaller
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than the matched allele.
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referring to exact matches. Whenever several CDSs from the same genome match a single or
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multiple alleles of the same locus with 100% DNA similarity during the first DNA sequence
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comparison, the *NIPHEM* tag is attributed.
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.. image:: /_static/images/NIPH_NIPHEM.png
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:width: 1400px
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:align: center
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- *PAMA* - PAralogous MAtch. Attributed to CDSs that are highly similar to more than one locus.
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This type of classification allows the identification of groups of similar loci in the
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schema that are classified as paralogous loci and listed in the ``paralogous_counts.tsv`` and
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``paralogous_loci.tsv`` files.
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.. image:: http://i.imgur.com/4VQtejr.png
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:width: 700px
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:align: center
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.. image:: /_static/images/PAMA.png
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:width: 1400px
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:align: center
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- *ALM* - Alleles 20% Larger than the length Mode of the distribution of the matched
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loci (CDS length > (locus length mode + locus length mode * 0.2)) (see image below).
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*ALMs* it is important to remember that, although infrequently, the mode may change as
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more alleles for a given locus are called and added to a schema.
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.. image:: http://i.imgur.com/l1MDyEz.png
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:width: 700px
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:align: center
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.. image:: /_static/images/ASM_ALM.png
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:width: 1400px
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:align: center
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.. note::
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The *ALM* and *ASM* classifications impose a limit on size variation since for the

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