Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome

Table 4 SNVs found in four genes of interest

Gene	Base No.	Change	Sanger confirmation	Nucleotide substitution	Amino acid substitution	Sanger confirmation on M ₄	Nucleotide substitution in progeny ¹	Script confirmation ²
ALS-1	119	C > T	Yes	Heterozygous	A/V	Yes	2 homozygous	Yes⁺⁺
ALS-1	140	C > T	No	N/A	P/L	N/A	N/A	No
CLE	89	G > A	Yes	Heterozygous	G/D	Yes	3 heterozygous	Yes⁺⁺⁺
CLE	94	G > A	Yes	Heterozygous	E/K	Yes	1 homozygous, 1 heterozygous	No
CLE	134	G > A	Yes	Heterozygous	R/H	Yes	1 homozygous	Yes⁺⁺⁺
ALS-2	26	G > A	No	N/A	G/E	N/A	N/A	No
ALS-2	43	G > A	Yes	Heterozygous	E/K	Yes	2 homozygous	No
ALS-2	100	G > A	No	N/A	E/K	N/A	N/A	No
ALS-2	161	C > T	Yes	Heterozygous	A/V	Yes	2 homozygous	Yes⁺⁺⁺
ALS-2	161	C > T	Yes	Homozygous	A/V	Yes	2 homozygous	Yes⁺
UGT	27	C > T	No	N/A	P/S	N/A	N/A	No
UGT	33	C > T	No	N/A	H/Y	N/A	N/A	No
UGT	81	C > T	Yes	Homozygous	L/F	Yes	3 homozygous	Yes⁺⁺⁺
UGT	99	G > A*	Yes	Heterozygous	E/STOP	Yes	3 heterozygous	N/A
UGT	99	G > A*	Yes	Heterozygous	E/STOP	Yes	2 heterozygous	N/A
UGT	184	G > A	Yes	Heterozygous	G/E	Yes	1 homozygous, 1heterozygous	No

^*Mutation was found by looking at intersecting pools with frequencies below the set threshold.
¹Six individuals from progeny examined per mutation.
²The frequencies of the variants were used to run a Phyton script which automatically detects the source individual bearing the mutation (Additional file 8). Parameters used in the script were: 2 lower SD cutoff, 10 upper SD cutoff, 1 min. pools. N/A rows were not picked by the script since they were found by a different methodology. The confirmed points by the script had confidence intervals of: ⁺75%, ⁺⁺85% and ⁺⁺⁺99%.
Mutations on position 161 on ALS-2 and 99 on UGT were found in two different individuals.

ISSN: 1746-4811