Identifying genes within pathways in unannotated genomes with PaGeSearch

Table 2.

The assembly statistics of the genomes used for validation

Archetype species Species Assembly level Contig number Total length N50 L50 No. per 100 kb
Homo sapiens Mus musculus Chromosome 61 2,728,222,451 130,530,862 9 2697.8
Homo sapiens Mus musculus Scaffold 12,661 2,801,301,292 1,291,016 585 9412.4
Homo sapiens Mus musculus Contig 224,709 2,477,635,466 24,821 29,731 0
Danio rerio Oryzias latipes Chromosome 25 734,057,086 31,218,526 11 66.9
Danio rerio Oryzias latipes Scaffold 298 772,952,521 31,949,249 12 11.6
Danio rerio Oryzias latipes Contig 2762 737,644,925 971,613 205 0
Arabidopsis thaliana Solanum tuberosum Chromosome 13 810,654,046 61,165,649 6 15,784.6
Arabidopsis thaliana Solanum tuberosum Scaffold 73,172 882,561,945 39,082 5913 1069.2
Arabidopsis thaliana Solanum tuberosum Contig 642,609 827,722,137 1487 144,345 0
Triticum aestivum Ozyra sativa Chromosome 63 375,049,285 29,958,434 6 31.53
Triticum aestivum Ozyra sativa Scaffold 12 375,082,798 30,085,288 6 2.27
Triticum aestivum Ozyra sativa Contig 304 392,277,955 27,391,607 7 0

This Article

  1. Published in Advance June 10, 2024, doi: 10.1101/gr.278566.123 Genome Res. 34: 784-795

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