A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Gurgul, Artur; Jasielczuk, Igor; Ropka-Molik, Katarzyna; Semik-Gurgul, Ewelina; Pawlina-Tyszko, Klaudia; Szmatoła, Tomasz; Szyndler-Nędza, Magdalena; Bugno-Poniewierska, Monika; Blicharski, Tadeusz; Szulc, Karolina; Skrzypczak, Ewa; Krupiński, Jędrzej

doi:10.1186/s12863-018-0681-0

BMC Genomic Data

Table 6 Statistics for the most significant core haplotypes being under selection and belonging to separate core regions in the analyzed breeds

From: A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Breed	Chr	Start Base	End Base	Size (kb)	Hap frequency	EHH	REHH	REHH P-Value	Genes directly overlapping with core haplotypes^a
PL	1	17,474,143	17,532,523	58.38	0.33	0.77	10.45	0.000902	LOC100152956, LOC100621885, LOC100512136, HOXB2, ZNF22, LOC100739279, C10orf10, RASSF4, LOC100157415, HOXB1, ALG6, HOXB3, ALOX5, LOC100523276, HOXB4, MARCH8
	2	18,722,196	18,775,121	52.925	0.31	0.53	10.91	0.00074
	2	18,850,395	18,872,659	22.264	0.31	0.45	12.46	0.0004
	2	42,642,528	42,708,543	66.015	0.64	0.60	9.68	0.000318
	6	137,335,517	137,534,028	198.511	0.27	0.79	10.35	0.000892
	7	87,029,852	87,066,927	37.075	0.59	0.88	7.79	0.000858
	7	115,164,638	115,233,642	69.004	0.39	0.89	10.21	0.000526
	8	33,740,426	33,760,858	20.432	0.34	0.88	16.21	0.000108
	10	32,485,201	32,589,926	104.725	0.60	0.53	7.74	0.000902
	12	24,427,829	24,643,031	215.202	0.27	0.64	11.03	0.000668
	12	24,696,740	24,812,751	116.011	0.27	0.64	10.70	0.000768
	13	211,907,795	211,989,807	82.012	0.48	0.48	9.93	0.00091
	14	98,887,138	99,642,277	755.139	0.42	0.93	10.94	0.00039
PUL	1	279,545,606	279,701,487	155.881	0.52	0.83	5.87	0.000374	PRKCQ, TERF1, FAM71F2, SBSPON, IMPDH1, LRP5
	1	279,545,606	279,701,487	155.881	0.52	0.74	7.52	8.35E-05
	2	3,166,230	3,236,832	70.602	0.58	0.58	5.09	0.000578
	4	68,321,268	68,385,012	63.744	0.58	0.63	5.93	0.000245
	4	123,472,417	123,553,728	81.311	0.48	0.99	7.18	0.000199
	4	123,712,634	123,819,209	106.575	0.48	0.92	5.73	0.000706
	4	123,838,086	123,907,205	69.119	0.48	0.90	6.14	0.000485
	10	70,638,252	70,669,410	31.158	0.35	0.52	8.00	0.000812
	18	20,991,435	21,077,884	86.449	0.77	0.55	4.22	0.00071
ZW	1	283,594,245	283,667,732	73.487	0.93	0.65	2.91	0.000144	C1orf115, SUSD1, PRKCE, MARC2
	3	14,090,668	14,221,604	130.936	0.32	0.98	6.04	0.000686
	3	30,457,204	30,733,237	276.033	0.45	1.00	5.01	0.000792
	3	100,417,119	100,448,894	31.775	0.81	0.55	2.95	0.000719
	3	100,521,767	100,536,654	14.887	0.71	0.69	4.08	0.000211
	3	100,521,767	100,536,654	14.887	0.71	0.70	3.88	0.000295
	8	141,594,565	141,644,208	49.643	0.46	0.80	5.73	0.000349
	8	141,594,565	141,644,208	49.643	0.46	0.98	5.49	0.000457
	10	12,274,858	12,388,946	114.088	0.27	1.00	5.98	0.000988
	11	14,256,201	14,501,882	245.681	0.32	1.00	8.03	0.000107
ZS	8	16,617,477	16,681,729	64.252	0.32	1.00	6.07	0.000145	UBE2F, RAMP1
	15	41,476,357	41,710,320	233.963	0.36	1.00	4.98	0.000291
	15	151,930,390	152,024,615	94.225	0.39	0.95	7.12	1.46E-05
	17	9,863,762	9,926,558	62.796	0.27	0.64	5.67	0.000355

^agenes with unassigned name were removed from the table

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