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Lucania parva LGs were numbered in descending order based on total length in cM.
Homoeologous chromosomes from acetocarmine and/or DAPI stained spreads were paired based on total length, arm ratio, and condensation pattern.
The sequencing depth was estimated based on total length of the reads used in the assembly divided by total size of transcriptome assemblies.
In spite of the remarkable gene loss, genome sizes of Alnus and Elaeagnus query strains were larger than would be expected based on total length of the absent genes.
Based on total length, number of scaffolds/contigs, largest scaffold/contig length, and scaffold/contig N50, HGAP2 outperformed the other approaches for both scaffolds (Table 1) and contigs (Table 2).
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The expected values are computed based on total lengths of the predefined genomic features.
InParanoid analyses identified 758 4-taxa orthologs (ABCD), an additional 645 3-taxa orthologs (BCD) and 3437 ortholog groups with sequences from only clades C and D. After filtering based on total tree length (# substitutions per codon), 611 ortholog groups were analyzed with all 4 taxa represented (average tree length = 4.1) and 528 were analyzed with 3 taxa (average tree length = 2.5).
Secondly, the sequencing data from the cycloheximide-treated sample were used to calculate overall coverage (based on total read length) and an RPKM value.
Based on total ungapped length of chromosomes, HM density appeared particularly homogeneous among human autosomes (249.3 ± 10.6 HM/Mb) but the X chromosome exhibited a lower density (207.1 HM/Mb).
In spite of these remarkable levels of gene loss, PFGE revealed that actual genome sizes of Alnus and Elaeagnus query strains were not as small as expected based on total LCR gene length.
However, when we analyzed PC species based on total acyl chain length or saturation level there were modest but statistically significant changes in the percentage of PC molecules with total acyl chain lengths of 32 or 34 carbons (Fig. 3C) and 0, 1, or 2 total double bonds (Fig. 3D), where FHV infection increased the fraction of PC molecules with longer unsaturated acyl chains.
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