<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">It’s an internal debugging related value used in the beta. It has no meaning for the general user and will eventually disappear.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 12, 2018, at 9:59 AM, Jennifer Anderson <<a href="mailto:jennifer.anderson@ebc.uu.se" class="">jennifer.anderson@ebc.uu.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Hello,</div>
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<div class="">I am working on the ab initiio annotation of a fungal genome, taking advantage of cDNA and protein evidence from other species. I am looking at my gff file following my first full attempt (hmm files from snap trained 2x, and GenemarkES).</div>
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<div class="">I have not found information on what it means “merge_warning=1” at the end of the ID line, as in the example below. Out of 6834 ID lines that include AED scores in this gff file, 5441 contain this warning. I would appreciate it if someone could
point me in the right direction.</div>
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<div class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre"> </span>
maker<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre">
</span>9255<span class="Apple-tab-span" style="white-space:pre"> </span>9992<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43</div>
<div class=""><font color="#ff2600" class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre">
</span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>mRNA<span class="Apple-tab-span" style="white-space:pre">
</span>9255<span class="Apple-tab-span" style="white-space:pre"> </span>9992<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;Parent=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|220;_merge_warning=1</font></div>
<div class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre"> </span>
maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre">
</span>9838<span class="Apple-tab-span" style="white-space:pre"> </span>9992<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:2;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1</div>
<div class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre"> </span>
maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre">
</span>9255<span class="Apple-tab-span" style="white-space:pre"> </span>9762<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:1;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1</div>
<div class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre"> </span>
maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre">
</span>9838<span class="Apple-tab-span" style="white-space:pre"> </span>9992<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>0<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1</div>
<div class="">000030F|arrow<span class="Apple-tab-span" style="white-space:pre"> </span>
maker<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre">
</span>9255<span class="Apple-tab-span" style="white-space:pre"> </span>9762<span class="Apple-tab-span" style="white-space:pre">
</span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">
</span>1<span class="Apple-tab-span" style="white-space:pre"> </span>ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1</div>
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<div class="">Best,</div>
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<div class="">Jenni</div>
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