@@ -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: 700 px
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- :align: center
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+ .. image :: /_static/images/PLOT5_PLOT3_LOTSC .png
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+ :width: 1400 px
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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.
@@ -293,14 +293,19 @@ The column headers stand for:
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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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+
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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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+
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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: 700 px
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- :align: center
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+ .. image :: /_static/images/PAMA .png
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+ :width: 1400 px
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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).
@@ -312,9 +317,9 @@ The column headers stand for:
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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: 700 px
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- :align: center
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+ .. image :: /_static/images/ASM_ALM .png
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+ :width: 1400 px
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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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