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Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, what does "Genes not located to the genome" mean?

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    $\begingroup$ I guess that the genes not located to the genome are the ones which cannot be mapped to a particular chromosome but are a part of some unmapped contig. You can see that from the GTF file but the figure does not match the stats shown here. In fact the stats page reports a total of 32078 genes records but the GTF only has 17716 (which is same as the genes located to the genome including unmapped contigs and mitochondria). So I guess the other genes are just present in the transcriptome assembly and are not mapped to any genome contig $\endgroup$ – WYSIWYG Dec 15 '15 at 6:11
  • $\begingroup$ @WYSIWYG it is related to genes and phenotypes from literature prior to having the sequenced genome. $\endgroup$ – AMR Dec 15 '15 at 16:53
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EDIT

Personal correspondence to representative at FlyBase.org

In FlyBase we have been gathering information about genes and phenotypes for over 20 years including information from papers and resources older than that. We annotate gene models on the Drosophila melanogaster genome assembly and when possible associate those annotations with other information (eg. phenotype, function etc) that is known about the gene. However, in some cases, especially for genes and phenotypes that were described in the older literature before the genome was sequenced we still have some information about those genes but have been unable to associate that information with a genome annotation. Those are what we call unlocalized genes (i.e. those without a annotation on the genome).

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