Table 3.
S. thermophilus strain identification by ORI, with and without merge index, in a balanced mixture of four or six strains more or less genetically close, by using 1000, 4000 or 16 000 sequencing reads
Best results are in bold type. Values of Hamming distance (0=perfect identification); MCC: Matthews correlation coefficient (1=perfect correlation); Ambiguity: number of strains identified/number of strains present.
|
(a) Global identification results (mean over all 90 experiments): |
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|---|---|---|---|---|---|---|
|
Method |
ORI |
ORI_merge |
||||
|
Distance |
0.52 |
0.41 |
||||
|
(MCC/Ambiguity) |
0.66/0.63 |
0.92/0.91 |
||||
|
(b) Heterogeneity, mean results (variable number of strains mixed): |
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|
Method |
ORI |
ORI_merge |
||||
|
Number of strains |
4 |
6 |
4 |
6 |
||
|
Distance |
0.73 |
0.31 |
0.53 |
0.29 |
||
|
(MCC/Ambiguity) |
0.70/0.65 |
0.65/0.56 |
0.94/0.93 |
0.96/0.96 |
||
|
(c) Data quantity, mean results (variable number of .fastq reads): |
||||||
|
Method |
ORI |
ORI_merge |
||||
|
Number of reads |
1000 |
4000 |
16 000 |
1000 |
4000 |
16 000 |
|
Distance |
0.17 |
0.8 |
0.6 |
0 |
0.43 |
0.8 |
|
(MCC/Ambiguity) |
0.55/0.44 |
0.64/0.64 |
0.78/0.80 |
0.86/0.77 |
0.93/0.92 |
0.98/1.05 |
|
(d) Resolution power, mean results (variable proximity between strains within the mixture): |
||||||
|
Method |
ORI |
ORI_merge |
||||
|
Proximity |
Distant |
Medium |
Close |
Distant |
Medium |
Close |
|
Distance |
0.10 |
1.17 |
0.30 |
0 |
0.90 |
0.33 |
|
(MCC/Ambiguity) |
0.75/0.73 |
0.61/0.68 |
0.6/0.47 |
0.93/0.89 |
0.87/0.85 |
0.97/1 |