Genomic Region Containing Toll-like Receptor Genes Has a Major Effect on IgM (Natural) Antibodies in Chickens


Supplementary Table 1.

Distribution of SNP used in this study over the chicken genome. The table shows: name of the chromosome (chromosomes 1-28 and 30-33, linkage group LGE64, sex chromosomes W and Z, and unplaced), total length of the chromosome (in basepair), the number of SNP on the chromosome, the number of monomorphic SNP (fixed) removed after quality control (step 1), the number of SNP removed after quality control (step 2-4), the number of SNP used in the genome-wide association studies. 



  Table is based on Gallus_gallus-5.0. 


						Supplementary Material
	Supplementary Table 1. continued				
				# SNP		
	Name	Total length (bp)	All	Fixed a Cleaned	Used
	21	7,159,517	936	522	103	311
	22	5,435,368	473	319	45	109
	23	6,289,313	761	# SNP 401	119	241
	Name 24	Total length (bp) 6,631,702	All 886	Fixed a Cleaned 510 89	Used 287
	1 25	210,673,733 3,644,590	8,651 240	5,470 169	757 10	2,424 61
	2 26	158,710,615 5,546,572	6,574 827	4,418 502	433 72	1,723 253
	3 27	116,920,747 6,304,838	4,953 613	3,261 423	523 34	1,169 156
	4 28	96,543,418 5,243,714	4,036 796	2,336 522	358 42	1,342 232
	5 30	63,034,728 224,321	2,640 0	1,660 -	216 -	764 -
	6 31	37,500,173 168,864	2,089 0	1,115 -	179 -	795 -
	7 32	38,707,053 253,552	2,177 0	1,332 -	187 -	658 -
	8 33	32,086,491 3,756,441	1,700 0	898 -	149 -	653 -
	9 LGE64	25,237,187 1,217,975	1,426 39	770 28	106 1	550 10
	10 W	21,385,625 7,082,455	1,618 11	941 11	187 0	490 0
	11 Z	21,449,822 88,942,393	1,577 3,058	1,028 2,966	146 88	403 333
	12 unplaced	21,002,089 138,546,488	1,640 929	1,126 508	232 40	282 52
	13 Total	19,897,466 1,230,241,782 57,636 37,053 1,437 1,028	101 5,005 15,578 308
	14	16,681,244	1,234	736	105	393
	15	13,353,506	1,258	940	131	187
	16	1,058,524	35	20	5	10
	17	11,686,891	1,055	646	163	246
	18	11,426,502	1,087	734	129	224
	19	10,716,916	1,011	467	137	407
	20	15,720,949	1,869	1,246	118	505
						3

a Monomorphic SNP
T V L Berghof, M H P W Visker, J A J Arts, H K Parmentier, J J Van Der Poel, A L J Vereijken, H Bovenhuis
Genomic Region Containing Toll-like Receptor Genes Has a Major Effect on IgM (Natural) Antibodies in Chickens