A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing

BMC Genomics

Table 5 The designed primers for amplification and sequencing of the chosen regions

Chromosome	Orientation	Name	Sequence 5′3’	Length	Tm	GC	Start	End	Amplifying length	N mismatches	Mismatch type
1	F	chr1_reg1_F	AAGCCCTCGGAGTAGCTTTC	20	59.46	55	109711755	109711774	397	3	3 SNV
1	R	chr1_reg1_R	GGCTGGAATCAATAAGCCCC	20	58.67	55	109712151	109712132	397	3	3 SNV
1	F	chr1_reg2_F	TGATGGACAGGATGGAGTTGTAG	23	59.55	47.83	109759300	109759322	85	1	1 INDEL
1	R	chr1_reg2_R	GAGCTGGACTCTTACCGCCTA	21	61.02	57.14	109759384	109759364	85	1	1 INDEL
2	F	chr2_reg1_F	GTGGTCACGGACATGCAGA	19	60.01	57.89	85663428	85663446	344	1	1 INDEL
2	R	chr2_reg1_R	CTGAGCGCTACTCCGTCATC	20	60.32	60.00	85663771	85663752	344	1	1 INDEL
2	F	chr2_reg2_F	CTCTGGACAGAGAGTATTTGGTTG	24	58.83	45.83	233671510	233671533	370	1	1 INDEL
2	R	chr2_reg2_R	AGGTGGGAGAAATACCAGCAC	21	59.72	52.38	233671879	233671859	370	1	1 INDEL
6	F	chr6_F	TTTAAGAAGGCAGGGGATTGCT	22	59.96	45.45	160246431	160246452	490	3	3 SNV
6	R	chr6_R	GCAACTTAAGCCTTCACCAGT	21	58.77	47.62	160246920	160246900	490	3	3 SNV
10	F	chr10_F	CCTGGAGACTTGCCTTGACC	20	60.32	60	101010511	101010530	233	1	1 INDEL
10	R	chr10_R	CCTCTACAAGACGTGCCAGT	20	59.40	55	101010743	101010724	233	1	1 INDEL
13	F	chr13_F	AAGCTCTTGATGCGGTGGTT	20	60.25	50	49792463	49792482	330	1	1 INDEL
13	R	chr13_R	CACGTATAGCCCGGCGAA	18	59.59	61.11	49792792	49792775	330	1	1 INDEL
22	F	chr22_F	CGAGGGCCCCATATAGGAGA	20	59.96	60	37973603	37973622	408	1	1 INDEL
22	R	chr22_R	GAGTTGGACCAGTACCTGCC	20	60.04	60	37974010	37973991	408	1	1 INDEL

ISSN: 1471-2164