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. 2015 Mar 14;11:19. doi: 10.1186/s13007-015-0062-x

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.