Table 4.
Mapping of Illumina-sequenced genomes of the 202 L5 strains to the M. tuberculosis H37Rv (L4) genome and complete genomes of 3 L5 strains from Benin, The Gambia and Nigeria (mapping statistics/estimates). The best mapping results (numbers) are written in bold. When the best mapping result has been obtained for PcbL5Nig as the reference, the next best result is also written in bold (as PcbL5Nig compared to the other 2 PcbL5 genomes missed a 30-gene region)
|
H37Rv |
PcbL5Ben |
PcbL5Gam |
PcbL5Nig |
|
|---|---|---|---|---|
|
Reads |
||||
|
Mean of percentage L5 reads mapped to |
96.9 |
97.5 |
97.3 |
96.5 |
|
Mean of unambiguous coverage mean |
122.3 |
123.2 |
123.3 |
123.0 |
|
Bases |
||||
|
Mean of percentage unambiguous total bases |
98.0 |
98.8 |
98.9 |
98.2 |
|
Mean uncovered |
30 599.0 |
18 916.7 |
14 766.4 |
35 340.4 |
|
Mean SNP |
2209.7 |
529.5 |
513.0 |
503.3 |
|
Mean deletions |
374.1 |
96.5 |
96.4 |
97.9 |
|
Mean insertions |
239.5 |
77.0 |
107.6 |
60.8 |
|
Mean substitutions (including stop codons) |
1193 |
0 |
0 |
0 |
|
Genes |
||||
|
Mean of percentage gene mapped (presence) |
99.59 |
99.71 |
99.79 |
99.76 |
|
L5 illumina having all the ref. genome genes, % ( n =202) |
0 |
2 (4) |
7.4 (15) |
0 |
|
Mean gene count difference between L5 Illumina-sequenced genomes (gene count per Illumina-sequenced genome minus minimum gene count) |
30.3 |
38.2 |
34.4 |
32.8 |