Using short read sequencing to characterise balanced reciprocal translocations in pigs

BMC Genomics

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

Animal	Karyotype	Coverage	DELLY out	Basic filt	Final filt^a	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(FN^b)
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

^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
^b FN False negative

ISSN: 1471-2164