Concentration values output by the QuantaSoft software for the 130 ddPCR assays. Sample: the DNA sample used for that assay; primer_pair: the identifier of the primer pair that was used for that assay; concentration: the concentration (in number of DNA templates per μl) measured for that assay. (CSV 2 kb)

Primer3 settings file used for the primer design of the PCR and ddPCR primers. (TXT 955 bytes)

Description of the primers used for the PCR and ddPCR assays. pair_id: the identifier attributed to a particular primer pair; chromosome: the chromosome on which the intended target of the primer pair is located; start_pos: the starting position of the intended target of the primer pair on the chromosome reference sequence; end_pos: the end position of the intended target of the primer pair on the chromosome reference sequence; amplicon_length: the predicted amplicon length of the intended target; forward_primer_sequence: the sequence of the forward primer; reverse_primer_sequence: the sequence of the reverse primer. (CSV 4 kb)

Description of the primers used for the PCR and ddPCR assays. pair_id: the identifier attributed to a particular primer pair; chromosome: the chromosome on which the intended target of the primer pair is located; start_pos: the starting position of the intended target of the primer pair on the chromosome reference sequence; end_pos: the end position of the intended target of the primer pair on the chromosome reference sequence; amplicon_length: the predicted amplicon length of the intended target; forward_primer_sequence: the sequence of the forward primer; reverse_primer_sequence: the sequence of the reverse primer. (CSV 4 kb)

Concentration values output by the QuantaSoft software for the 130 ddPCR assays. Sample: the DNA sample used for that assay; primer_pair: the identifier of the primer pair that was used for that assay; concentration: the concentration (in number of DNA templates per μl) measured for that assay. (CSV 2 kb)

Copy number variants found in the 19 individuals subjected to aCGH. ID: the identifier of the mutant; CNV_type: the type of CNV (homdel = homozygous deletion, hetdel = hemizygous deletion, dup = duplication); chr: the chromosome on which the CNV is located; start: the starting position of the CNV; end: the end position of the CNV; kbp: the estimated size of the CNV in kbp; n_probes: the number of aCGH probes supporting this CNV; mean_log2: the mean log2 ratio of the probes across this CNV; found_by_GBS: whether or not this CNV was detected by the GBS approach. (CSV 6 kb)

Copy number variants found in the 19 individuals subjected to aCGH. ID: the identifier of the mutant; CNV_type: the type of CNV (homdel = homozygous deletion, hetdel = hemizygous deletion, dup = duplication); chr: the chromosome on which the CNV is located; start: the starting position of the CNV; end: the end position of the CNV; kbp: the estimated size of the CNV in kbp; n_probes: the number of aCGH probes supporting this CNV; mean_log2: the mean log2 ratio of the probes across this CNV; found_by_GBS: whether or not this CNV was detected by the GBS approach. (CSV 6 kb)

Copy number variants found in the 79 mutants sequenced by GBS using the two combined libraries. ID: the identifier of the mutant; CNV_type: the type of CNV (homdel = homozygous deletion, hetdel = hemizygous deletion, dup = duplication); chr: the chromosome on which the CNV is located; start: the starting position of the CNV; end: the end position of the CNV; kbp: the estimated size of the CNV in kbp; n_bins: the number of 1-kb bins supporting this CNV; mean_log2: the mean log2 ratio of the bins across this CNV; validated_by_CGH: whether or not this CNV was validated by the aCGH dataset; validated_by_PCR: whether or not this CNV was validated by the PCR/ddPCR assays. (CSV 11 kb)

Copy number variants found in the 79 mutants sequenced by GBS using the two combined libraries. ID: the identifier of the mutant; CNV_type: the type of CNV (homdel = homozygous deletion, hetdel = hemizygous deletion, dup = duplication); chr: the chromosome on which the CNV is located; start: the starting position of the CNV; end: the end position of the CNV; kbp: the estimated size of the CNV in kbp; n_bins: the number of 1-kb bins supporting this CNV; mean_log2: the mean log2 ratio of the bins across this CNV; validated_by_CGH: whether or not this CNV was validated by the aCGH dataset; validated_by_PCR: whether or not this CNV was validated by the PCR/ddPCR assays. (CSV 11 kb)

Copy number of templates amplified by 37 primer pairs in mutant and control lines as assessed by a ddPCR assay. ID: the identifier of the mutant; CNV_type: the type of CNV (homdel = homozygous deletion, hetdel = hemizygous deletion, dup = duplication); chr: the chromosome on which the CNV is located; start: the starting position of the CNV; end: the end position of the CNV; primer_pair: the identifier of the primer pair that was used for that assay; mutant_conc: the concentration (in number of DNA templates per μl) measured in the mutant for that assay; mutant_ref: the concentration (in number of DNA templates per μl) measured using reference primer pair BY in that mutant; mutant_n: the copy number of the templates amplified by primer_pair in the mutant as determined by dividing mutant_conc by mutant_ref; control_conc: the concentration (in number of DNA templates per μl) measured in the control for that assay; control_ref: the concentration (in number of DNA templates per μl) measured using reference primer pair BY in the control; control_n: the copy number of the templates amplified by primer_pair in the control as determined by dividing control_conc by control_ref; ratio: the ratio of the copy number of the mutant to the copy number of the control for the templates amplified by primer_pair. (CSV 4 kb)