Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

Table 3 Repeatability measures for each duplicate pair after 3rd, 4th and 5th step of the variant validation procedure and following supertype classification

	Read no	Verified alleles / ST				Unverified alleles / ST				Repeatability
		S3	S4	S5	ST	S3	S4	S5	ST	S3	S4	S5	ST
duplicate-1	528 - 668	31	28	28	9	120	10	0	0	0.21	0.74	1	1
duplicate-2	387 - 418	29	29	28	11	71	14	0	0	0.29	0.67	1	1
duplicate-3	322 - 501	22	22	22	13	54	6	0	0	0.29	0.79	1	1
duplicate-4	471 - 507	26	25	22	9	71	7	0	0	0.27	0.78	1	1
duplicate-5	267 - 484	21	21	21	8	40	6	0	0	0.34	0.78	1	1
duplicate-6	276 - 456	21	20	20	10	52	4	0	0	0.29	0.83	1	1
duplicate-7	288 - 319	23	23	22	10	32	4	1	0	0.42	0.85	0.96	1
duplicate-8	208 - 455	21	21	20	10	50	13	2	0	0.3	0.62	0.91	1
duplicate-9	272 - 289	27	26	23	10	34	3	3	1	0.44	0.89	0.88	0.91
duplicate-10	240 - 471	21	21	18	10	66	20	3	1	0.24	0.51	0.86	0.91
duplicate-11	230 - 236	24	24	21	11	26	6	4	1	0.48	0.8	0.84	0.92
duplicate-12	240 - 570	20	20	19	10	50	22	4	2	0.29	0.48	0.83	0.83
*Average*	287 - 448	24	23	22	10	56	9.6	1.4	0.4	0.32	0.73	0.94	0.96

ST – supertypes; read no - the number of reads per sample. Verified alleles/supertypes stand for the number of identical alleles/supertypes between the duplicate samples. Unverified alleles/supertypes represent the number of alleles/supertypes that were found in one of the samples and indicate non-identical genotypes. Repeatability was calculated as the ratio of verified alleles/supertypes to the total number of alleles/supertypes for each duplicate. A repeatability value of 1 signifies identical genotypes. For a duplicate each measurement was calculated four times - after the 3rd, 4th and 5th steps of the variant validation procedure, and following supertype classification. The average values for each measure are provided in the bottom row.