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Table 1 Comparison of alignment methods and cFinder to manual approach

From: cFinder: definition and quantification of multiple haplotypes in a mixed sample

Sample (no.) Clone variants Manual cFinder (AVA) cFinder (CLCbio)
% Hits % Hits % Hits
1 c.749 G>A 22.0 14,956 23.3 15,611 22.43 14,745
  c.757 T>C 26.5 18,458 30.6 20,886 29.39 19,604
2 c.749G>A, c.943A>G, c.1497A>G 15.7 4748 6.4 4362 6.21 4066
  c.749G>A, c.949T>A, c.1497A>G 4.1 1240 2.4 1641 2.3 1522
  c.749G>A, c.1497A>G 22.7 6864 7.1* 4145 6.7* 3729
  c.943A>G, c.1497A>G 17.1 16,237 12.6 9183 12.5 8715
  c. 949T>A, c.1497A>G 3.3 3128 4.5 3342 4.6 3240
  c.1497A>G 45.2 26,522 61.2* 35,867* 61.3* 33,804
  c.749G>A, c.949T>A 3.4 2519 3.5 2488
  c.749G>A 13.9 7996 14.2 8074
  c.749G>A, c.943A>G 10.8 7838 10.9 7692
  c.943A>G 4.0 3483 4.2 3574
  c.949T>A 1.1 991 1.2 1023
3 c.1375G>A, c.1423_1424ins35 6.2 3495 5.9 3186 6.4 3019
  c.1375G>A 90.9 51,247 90.9 51,891 87.9 42,693*
4 c.730A>G 20.3 9887 27.5 17,769 27.5 17,483*
5 c.756G>T, c.1086_1270del185 5.4 1407 6.2 1406 6.8 1490
  c.756G>T, c.1423_1424ins35 1.0 160 1.6 244 0.2** 30
  c.756G>T 41.0 10,845 58.9* 12,446* 57.3* 11,545
  c.1423_1424ins35 1.6 244 1.6 235
  c.1086_1270del185 2.7 727 2.6 625 2.6 611
  c.888_919del32 1.6 427 0.9** 220 0.2** 40
6 c.756G>>T, c.1086_1270del185 20.4 8151 14.1 7922 14.1 7702
  c.1086_1270del185 6.3 4008 4.6 2828
  c.756G>T 64.6 32,472 65.0 31,932 63.3 30,093
7 c.756G>T 51.2 38,883 62.3* 38,726 61.5* 37,336
8 c.838_1378del540, c.1423_1424ins35 98.4 49,425 85.7* 47,729
  c.1423_1424ins35 2.1 1187
  c.838_1378del540 10.8 6013
9 c.825G>A 2.2 229 3.1 269 3.0 250
10 c.1086_1270del185, c.1423_1424ins35 1.3 278 0.5** 132 0.5** 116
  c.944C>T, c.1086_1270del185 9.1 2260 7.5 2215 5.3 1548
  c.944C>T 30.6 9778 33.7 10,069 34.3 10,061
  c.1086_1270del185 12.1 3278 10.4 3026 7.4 2164
  c.1423_1424ins35 2.1 460 1.9 384 1.8 375
  1. Sample and found clone variants are listed with their percentage of occurrence and the hits (absolute number of reads with that variant), comparing manual detection with automated analysis with cFinder with two different alignment software products. Results marked with one star (*) show intense deviation from manual findings, numbers marked with two stars (**) fell below threshold of 1 %. If clone was not detected it is marked with a dash (–)