| Number of required occurences | Description | |||||||||
| mipe | exactly one | |||||||||
| version | exactly one | version number of the MIPE format | ||||||||
| pcr | one or more | one for each PCR product | ||||||||
| id | exactly one | ID of the PCR product | ||||||||
| modified | one or more | dates that this record has been modified | ||||||||
| project | zero or more | project(s) that this record belongs to | ||||||||
| researcher | one or more | researcher(s) involved in designing/running the PCR | ||||||||
| species | one or more | species on which the PCR experiment is performed | ||||||||
| design | exactly one | data pertaining to the design of the PCR | ||||||||
| source | exactly one | initial sequence on which the PCR primers were designed | ||||||||
| accession/file/seq | exactly one | reference to the source DNA sequence | ||||||||
| name | zero or one | e.g. gene-name | ||||||||
| species | zero or one | species on which the PCR experiment is performed | ||||||||
| type | zero or one | genomic or cDNA | ||||||||
| remark | zero or more | |||||||||
| range | zero or one | part of the source sequence that will be amplified by the PCR product (in nucleotide positions) | ||||||||
| seq | zero or one | sequence expected to be replicated (= part of the source sequence) | ||||||||
| primer1 | zero or one | forward primer | ||||||||
| oligo | zero or one | internal ID of oligo | ||||||||
| seq | zero or one | sequence of primer | ||||||||
| tm | zero or one | melting temperature of primer | ||||||||
| primer2 | zero or one | reverse primer | ||||||||
| oligo | zero or one | internal ID of oligo | ||||||||
| seq | zero or one | sequence of primer | ||||||||
| tm | zero or one | melting temperature of primer | ||||||||
| profile | zero or one | PCR profile | ||||||||
| name | zero or one | name of PCR profile | ||||||||
| predenaturation | zero or one | predenaturation step | ||||||||
| temp | exactly one | |||||||||
| time | exactly one | |||||||||
| cycle | zero or more | data for each cycle | ||||||||
| number | exactly one | number of cycles | ||||||||
| denaturation | exactly one | denaturation step | ||||||||
| temp | exactly one | |||||||||
| time | exactly one | |||||||||
| annealing | exactly one | annealing step | ||||||||
| temp | exactly one | |||||||||
| time | exactly one | |||||||||
| elongation | exactly one | elongation step | ||||||||
| temp | exactly one | |||||||||
| time | exactly one | |||||||||
| postelongation | zero or one | postelongation step | ||||||||
| temp | exactly one | |||||||||
| time | exactly one | |||||||||
| remark | zero or more | |||||||||
| use | zero or one | contains information on the results of a PCR resequencing experiment | ||||||||
| seq | exactly one | sequence | ||||||||
| revcomp | exactly one | whether or not this sequence is the reverse complementary of the sequence in the design part | ||||||||
| snp | zero or more | single-nucleotide polymorphisms | ||||||||
| id | exactly one | |||||||||
| pos | exactly one | position of the SNP on the use sequence | ||||||||
| pos_design | zero or one | position of the SNP on the design sequence | ||||||||
| pos_source | zero or one | position of the SNP on the sourcesequence | ||||||||
| amb | zero or one | ambiguity code of the SNP | ||||||||
| rank | zero or one | if found by polyphred: rank of the SNP (ranges from 1 to 6) | ||||||||
| assay | zero or more | SNP genotyping assay | ||||||||
| type | exactly one | either RFLP or SBE (single-base extension) | ||||||||
| id | exactly one | |||||||||
| enzyme | zero or one | if type was RFLP: restriction enzyme | ||||||||
| oligo | zero or one | internal ID of oligo | ||||||||
| specific | zero or one | if type was SBE: sequence of the SBE primer that is specific | ||||||||
| tail | zero or one | if type was SBE: sequence of optional tail that is non-specific | ||||||||
| strand | zero or one | if type was SBE: strand that the SBE primer will attach to (relative to the sequence in the use part) | ||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||
| sample | zero or more | if resequenced on different individuals | ||||||||
| id | zero or one | |||||||||
| file | zero or one | ab1-file containing the sequence for this particular individual | ||||||||
| genotype | zero or more | genotypes for this individual | ||||||||
| snp_id | exactly one | ID of a SNP as mentioned above | ||||||||
| amb | exactly one | ambiguity code for that SNP in this individual | ||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||
| remark | zero or more | |||||||||