Table 1.
Deletion Screen of CDC1551 Shows that TSTEP/Deletion Assembly Finds All Deletions >350 bp in Nonrepetitive Regions, with No False Deletion Cells
| H37Rv regions of at least 300 bp with no identical match in CDC1551 (to the nearest 60 bp) | Repetitive sequence family in probe set annotation | Similarity with any region by blast to CDC1551 (%) | Edges detectable by blast to CDC1551 (corresponding address in H37Rv is given) | Deletion in nonrepetitive region, with detectable edges >350 bp | Complete TSTEP/deletion assembly results for screen of CDC1551 | ||||||
| Start | Stop | Length | Start | Stop | Length | Start | Stop | Length | |||
| 333540 | 336300 | 2760 | PE/PGRS | 99.3 | No | ||||||
| 336360 | 339000 | 2640 | PE/PGRS | 97.1 | No | ||||||
| 835920 | 841080 | 5160 | PE/PGRS | 99.6 | No | ||||||
| 886500 | 887460 | 960 | 886541 | 887414 | 873 | Yes | 886427 | 887553 | 1127 | ||
| 1217460 | 1218180 | 720 | PE/PGRS | 72.9 | No | ||||||
| 2045040 | 2045400 | 360 | PE/PGRS | 95.0 | No | ||||||
| 2060280 | 2060700 | 420 | 87.4 | No | |||||||
| 2339220 | 2339640 | 420 | 2339258 | 2339503 | 245 | No | |||||
| 2381400 | 2383740 | 2340 | Overlaps PPE | 2381413 | 2383683 | 2270 | Yes | 2380893 | 2383514 | 2622 | |
| 2704260 | 2704920 | 660 | 2704308 | 2704805 | 497 | Yes | 2704242 | 2704695 | 454 | ||
| 3054660 | 3054960 | 300 | PE/PGRS | 3054720 | 3054906 | 186 | No | ||||
| 3122580 | 3123300 | 720 | 3122828 | 3123145 | 517 | Yes | 3122606 | 3123248 | 643 | ||
| 3501300 | 3501720 | 420 | PPE | 3501331 | 3501662 | 331 | No | ||||
| 3730860 | 3732180 | 1320 | PPE | 3730999 | 3732075 | 1076 | No | ||||
| 3732600 | 3735720 | 3120 | PPE | 3732653 | 3735632 | 2979 | No | ||||
| 3842280 | 3846600 | 4320 | Overlaps PPE | 3842305 | 3846512 | 4207 | Yes | 3842882 | 3846825 | 3944 | |
| 3894600 | 3894900 | 300 | PPE | 91.3 | No | ||||||
| 3895020 | 3895320 | 300 | PPE | 86.4 | No | ||||||
| 3933480 | 3934020 | 540 | PE/PGRS | 96.7 | No | ||||||
| 3934080 | 3936660 | 2580 | PE/PGRS | 89.9 | No | ||||||
| 3939720 | 3945120 | 5400 | PE/PGRS | 99.0 | No | ||||||
| 3946860 | 3950340 | 3480 | PE/PGRS | 69.2 | No | ||||||
| 3955440 | 3956100 | 660 | 3955464 | 3956100 | 636 | Yes | 3955252 | 3956433 | 1182 | ||
-
(TSTEP) Tandem Set Terminal Extreme Probability.
-
↵More than one region with 60% or more identity is found in this interval. A weighted average is reported.
-
↵There are only three probe pairs querying the 245-bp interval. A weak signal of P value <0.01 is measured for these probe pairs.
-
↵PPE locus at 2381069–2382490.
-
↵PPE loci at 3842235–3842765 and 3843032–3843730.
