Figure 1.
Comparison of SNP and INDELs detection tools based on different sequence assemblies.
Assemblies of KIM D27 sequences from either 454 only, Illumina only, or hybrid assemblies (454 + Illumina) were analyzed for SNPs and INDELs as described in Materials and Methods. The Venn diagram represents the number of identified differences in either CLC Genomics Workbench or Newbler either singly (purple or blue, respectively) or the overlap between both programs (darkened area).
Table 1.
Summary of sequencing results for Y. pestis KIM D27 and comparison with KIM10.
Figure 2.
A. Nucmer alignement of putative invasin gene from KIM 10+ and KIM D27.
Regions of homology are depicted as diagonal lines. The 289 bp repeat aligns with itself numerous times and results in the square pattern. B. PCR amplification of the invasin gene from KIM 10+ and KIM D27. The chromosomal region 4228610 – 4234900 was amplified from genomic DNA from either strain. The predicted 6,290 bp product was observed as the major product from KIM D27 (lanes 1 and 2), but a ladder effect was observed when KIM 10+ DNA was used (lanes 3 and 4).
Table 2.
Repeat expansion or reduction in Y. pestis KIM D27.
Table 3.
SNP/INDEL confirmed in Y. pestis KIM10+.
Table 4.
Search for conflicting INDELs in 454-only genomes.
Figure 3.
Instances of poly(A) and poly(T) in sequenced genomes.
All 4–9 bp poly(A) and poly(T) in published genomes were counted and plotted per kilobase in each genome.