Table 2 Read mapping statistics for Illumina (A) and nanopore libraries prepared with REPLI-g (B) and Sigma (C) WTA protocols. Reads were mapped using BWA-MEM with default settings (Illumina) or nanopore-specific (-x ont2d) settings. Columns are, respectively, NCBI accession numbers for each VEEV reference genome shown; total number of reads mapped to each reference; number of non-specific matches, number of perfect matches, average depth of coverage of non-zero coverage regions, percentage of reference genome covered by at least 1 read; number of regions in the reference with zero coverage; and total length of zero coverage regions.
Accession# | #Reads | NPM | Avg. DOC* | %Ref. Cov. | No. Zero Regions. | Total Zero Len. |
|---|---|---|---|---|---|---|
A. Illumina – BWA-MEM (default) | ||||||
KR260737 | 4073 | 2925 | 43.25 | 98.0% | 7 | 256 |
AF075251 | 1180 | 882 | 17.08 | 68.0% | 40 | 3594 |
KC344490 | 3 | 2 | 1.84 | 0.7% | 2 | 11333 |
KC344526 | 3 | 1 | 1.41 | 1.0% | 3 | 11308 |
KC344471 | 2 | 2 | 2 | 0.3% | 2 | 11328 |
KC344507 | 2 | 1 | 1.45 | 0.8% | 2 | 11050 |
DQ390224 | 1 | 0 | 1 | 0.5% | 2 | 11358 |
EEVCOMGEN | 1 | 1 | 1 | 0.5% | 2 | 11391 |
EEVNSPEPB | 1 | 1 | 1 | 0.7% | 2 | 11364 |
KC344475 | 1 | 1 | 1 | 0.3% | 2 | 11384 |
KC344522 | 1 | 1 | 1 | 0.4% | 2 | 11362 |
NC_001449 | 1 | 1 | 1 | 0.5% | 2 | 11391 |
B. Nanopore (REPLI-g) – BWA-MEM (-x ont2d) | ||||||
KR260737 | 9 | 9 | 2.44 | 16.0% | 3 | 9502 |
AF075251 | 3 | 3 | 1.37 | 10.0% | 2 | 10263 |
AF075258 | 1 | 1 | 1.00 | 0.6% | 1 | 11428 |
C. Nanopore (SIGMA) – BWA-MEM (-x ont2d) | ||||||
KR260736 | 45 | 45 | 14.65 | 0.02 | 2 | 11276 |
KR260737 | 25 | 25 | 1.68 | 0.55 | 7 | 5147 |
AF075251 | 4 | 4 | 1.08 | 0.11 | 4 | 10163 |
