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Table 2 Translocation output at various stages of the pipeline for 7 carriers and 15 non-carriers with negative RT results

From: Using short read sequencing to characterise balanced reciprocal translocations in pigs

Animal Karyotype Coverage DELLY out Basic filt Final filta Visual insp
Pig1 t(2;4) 32.6 59,865 1127 30 (15) 1 (2,4)
Pig2 t(6;8) 37.9 80,967 1426 56 (28) 1 (6,8)
Pig3 t(2;4) 33.4 70,794 1185 34 (17) 1 (2,4)
Pig4 t(2;4) 35.1 78,454 1175 38 (19) 1 (2,4)
Pig5 t(7;14) 37.2 79,418 1503 68 (34) 1 (7,14)
Pig6 t(2;4) 31.1 61,639 1067 38 (19) 1 (2,4)
Pig7 t(1;16) 30.3 64,583 1116 44 (22) 0(FNb)
Contr1 normal 33.5 70,326 1281 58 (29) 0
Contr2 normal 31.7 58,678 974 36 (18) 0
Contr3 normal 30.3 68,711 1009 32 (16) 0
Contr4 normal 28.8 42,268 788 24 (12) 0
Contr5 normal 30.7 70,738 1116 30 (15) 0
Contr6 normal 34.3 69,866 1295 50 (25) 0
Contr7 normal 31.2 49,269 873 32 (16) 0
Contr8 normal 29.1 66,194 1145 38 (19) 0
Contr9 normal 29.2 62,080 1118 34 (17) 0
Contr10 normal 28.9 41,329 556 16 (8) 0
Contr11 normal 29.4 48,292 810 34 (17) 0
Contr12 normal 29.1 65,296 1085 34 (17) 0
Contr13 normal 29.3 52,289 868 36 (18) 0
Contr14 normal 29.0 55,121 920 46 (23) 0
Contr15 normal 29.2 58,460 942 36 (18) 0
  1. a one of the filter criteria for the detected inter-chromosomal translocations was the presence of a matching pair, hence between brackets are the number of reciprocal pairs, i.e. the actual number of possible RTs
  2. b FN False negative