Fig 1.
Feature response curves (FRC) computed for all features (A) and low coverage features (B) (adapted from [32]). FRC are shown for HGAP, allpaths, dekkera_V1 (final assembly presented in [32]) and dekkera_V2 (assembly presented in this work). The decreased amount of features when removing the duplicated fragment of chromosome 1 in dekkera_V1 assembly is mostly attributed to the loss of regions below normal read coverage (B). Such regions are often indicative of incorrect repeat expansions made by the assembly program [32].
Fig 2.
Location of certain genes (A) and duplicated genes (B) on the chromosomes of CBS 11270.
Table 1.
Annotation details of the B. bruxellensis CBS 11270 nuclear genome.
Fig 3.
Number and location of variants on chromosomes of B. bruxellensis CBS 11270.
Y-axes represent the number of variants per 10,000 bp. Black bars show occurrence of variants. Red color denotes chromosome margins.
Table 2.
Statistics of variant analysis in heterozygous sites in genome of CBS 11270 and between genomes of CBS 11270 and CBS 2499.
Table 3.
Counts of different types of nucleotide transversions and transitions in heterozygous sites in the genome of CBS 11270 and between the genomes of CBS 11270 and CBS 2499.
Table 4.
Survey of the genes with the highest numbers of SNPs in CBS 11270 and CBS 2499.
Fig 4.
Distribution of indels of different size in heterozygous sites in the genome of CBS 11270 (A) and between genomes of CBS 11270 and CBS 2499 (B).
Table 5.
Duplicated genes revealed by CNV analysis and not identified in the genome assembly.
Table 6.
List of duplicated genes resolved by genome assembly.
Table 7.
Characterization of repeats in flanking regions of duplicated genes.
Table 8.
Genes in the B. bruxellensis CBS 2499 genome absent in the CBS 11270 genome.