Updated to 1,081,736 high coverage COVID-19 WGS from GISAID using BLASTDB version 5.
Run Date: 05/7/2021
Table 1. PSET analysis using SARS-CoV-2 as the intended target. Perfect True Positive (PT), True Positive (TP), and False Negative (FN) counts for various assays were produced in each run. The five Noblis assays were compared alongside with assays produced in the US including the Corman (four assays) and CDC (three assays) brands. Assays originating from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore were also used in this comparison. Algorithms were set to penalize Ns on the subject sequence. Internal improvement to the PSET algorithms and snakemake (Snakemake — Snakemake 6.2.1 documentation) pipeline implementations decreased the Type I and Type II error rates compared with previous versions. We no longer calculate off-target hits due to the continued stability of these values.
| Assay | PT | TP | FN | Percent True |
|---|---|---|---|---|
| Noblis.12 | 1055483 | 21103 | 220 | 99.98% |
| Noblis.40 | 1054779 | 22150 | 92 | 99.99% |
| Noblis.42 | 1066452 | 10448 | 25 | 100.00% |
| Noblis.44 | 1065821 | 10982 | 36 | 100.00% |
| Noblis.57 | 1062626 | 15899 | 103 | 99.99% |
| ncov_e_gene | 1072331 | 4201 | 216 | 99.98% |
| ncov_n_gene | 1048853 | 27418 | 152 | 99.99% |
| ncov_rdrp_1 | 0 | 1075806 | 1172 | 99.89% |
| ncov_rdrp_2 | 31 | 1076322 | 635 | 99.94% |
| cdc_n1 | 1038877 | 37797 | 12 | 100.00% |
| cdc_n2 | 1038361 | 37699 | 76 | 99.99% |
| cdc_n3 | 1036012 | 40716 | 16 | 100.00% |
| China_N | 358119 | 106799 | 609811 | 43.26% |
| China_ORF1ab | 1067798 | 8839 | 160 | 99.99% |
| France_nCoV_IP2 | 1058123 | 18653 | 90 | 99.99% |
| France_nCoV_IP4 | 1018659 | 58223 | 148 | 99.99% |
| HKU-N | 1048396 | 27363 | 69 | 99.99% |
| HKU-ORF1b-nsp14 | 1067524 | 9406 | 64 | 99.99% |
| Japan_NIID_2019-nCOV_N | 2 | 1075641 | 204 | 99.98% |
| Japan_NIID_WH-1_F24381 | 1062677 | 15456 | 234 | 99.98% |
| Japan_NIID_WH-1_F501 | 1063930 | 12551 | 75 | 99.99% |
| Japan_NIID_WH-1_F509 | 1053255 | 23074 | 242 | 99.98% |
| Japan_NIID_WH-1_Seq_F24383 | 1062389 | 14339 | 1659 | 99.85% |
| Japan_NIID_WH-1_Seq_F519 | 1050519 | 16955 | 9112 | 99.15% |
| Japan_WuhanCoV-spk1 | 1067642 | 10481 | 205 | 99.98% |
| Thailand_WH-NIC_N | 1057475 | 19183 | 71 | 99.99% |
| Chan-N | 1045151 | 30480 | 151 | 99.99% |
| Chan-ORF1ab | 41 | 1076321 | 73 | 100.00% |
| Chan-S | 1048072 | 27596 | 417 | 99.96% |
| Niu-E | 1065378 | 11145 | 229 | 99.98% |
| Won-E | 5 | 1076580 | 157 | 99.99% |
| Won-N | 1052374 | 23961 | 23 | 100.00% |
| Won-ORF1ab | 1068015 | 8946 | 12 | 100.00% |
| Won-S | 1065942 | 8601 | 721 | 99.93% |
| Yip-ORF1ab | 1066864 | 9538 | 63 | 99.99% |
| Young-N | 1 | 1076761 | 48 | 100.00% |
| Young-ORF1ab | 1061627 | 15000 | 358 | 99.97% |
| Young-S | 563864 | 44899 | 461606 | 56.87% |
| C1_COV_ORF1a | 1053672 | 18772 | 176 | 99.98% |
| C2_COV_ORF1b | 1047179 | 29732 | 19 | 100.00% |
| C3_COV_ORF3a | 953272 | 121543 | 346 | 99.97% |
| C4_COV_ORF8 | 589965 | 483426 | 1713 | 99.84% |
| C5_COV_S_gene | 1063209 | 15402 | 84 | 99.99% |