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@@ -694,6 +694,7 @@ <h2 id="output">Output</h2>
 <li><code>P.meta_info.json</code> - a JSON format file containing information about relevant parameters with which <code>oarfish</code> was run, and other relevant inforamtion from the processed sample apart from the actual transcript quantifications.</li>
 <li><code>P.quant</code> - a tab separated file listing the quantified targets, as well as information about their length and other metadata. The <code>num_reads</code> column provides the estimate of the number of reads originating from each target.</li>
 <li><code>P.infreps.pq</code> - a <a href="https://parquet.apache.org/"><code>Parquet</code></a> table where each row is a transcript and each column is an inferential replicate, containing the estimated counts for each transcript under each computed inferential replicate.</li>
+<li><code>P.ambig_info.tsv</code> - a tab separated file listing, for each transcript (in the same order in which they appear in <code>P.quant</code>) the number of uniquely mapped, ambiguously mapped, and total reads.  The quantification estimate for each transcript, in general, should reside between the number of uniquely aligned reads and the total number of reads (i.e. these provide, respectively lower and upper bounds for the number of reads assigned to each transcript).  Note that the total in this file is the total number of reads that align to this transcript with a sufficiently high alignment score --- it is <em>not</em>, in general, an estimate of the number of reads originating from this transcript as many of those reads can be multimapping and, in fact, potentially better described by other transcripts.</li>
 </ul>
 <h2 id="references">References</h2>
 <div class="footnote">