| accession |
ERA/SRA accession number for the sample if it was submitted |
| additional_argument |
any additional arguments that differ from the default |
| additional_methods |
any additional methods used to analyze the data |
| alt_annotations |
a list of additional annotations associated with this microhaplotype, e |
| alternate_identifiers |
a list of optional alternative names for the specimens |
| associations |
a list of associations with this marker, e |
| bioinformatics_method_name |
name of the collection of methods is called, e |
| bioinformatics_methods_id |
the index into the bioinformatics_methods_info list |
| bioinformatics_methods_info |
the bioinformatics pipeline/methods used to generated the amplicon analysis f... |
| bioinformatics_run_id |
the index into bioinformatics_run_info list |
| bioinformatics_run_info |
the runtime info for the bioinformatics pipeline used to generated the amplic... |
| bioinformatics_run_name |
a name to for this run |
| BioProject_accession |
an SRA bioproject accession e |
| chrom |
the chromosome name |
| chromosomes |
a list of chromosomes found within this genome |
| collection_country |
the name of country collected in, would be the same as admin level 0 |
| collection_date |
the date of the specimen collection, can be YYYY, YYYY-MM, or YYYY-MM-DD |
| creation_date |
the date of when the PMO file was created or modified, should be YYYY-MM-DD |
| date_measured |
the date the qpcr was performed, can be YYYY, YYYY-MM, or YYYY-MM-DD |
| demultiplexing_method |
the demultiplexing method used to separate raw reads from barcodes and primer... |
| denoising_method |
the method used to de-noise and/or cluster the raw reads |
| density_method |
the method of how this density was obtained |
| density_method_comments |
additional comments about how the density was performed |
| drug_usage |
Any drug used by subject and the frequency of usage; can include multiple dru... |
| end |
the end of the location, 0-based positioning |
| env_broad_scale |
the broad environment from which the specimen was collected, e |
| env_local_scale |
the local environment from which the specimen was collected, e |
| env_medium |
the environment medium from which the specimen was collected from |
| experiment_info |
a list of experiments of all the seq/amp of the specimens within this project |
| experiment_sample_id |
the index into the experiment_info list |
| experiment_sample_name |
a unique identifier for this sequence/amplification run on a specimen_name |
| experiment_samples |
a list of the microhaplotypes detected for a sample by targets |
| forward_primer |
the forward primer associated with this target |
| gene_name |
an identifier of the gene, if any, is being covered with this targeted |
| generation_method |
the generation method to create this PMO |
| genome_id |
the index to the genome in the targeted_genomes list that this location refer... |
| genome_version |
the genome version |
| geo_admin1 |
geographical admin level 1, the secondary large demarcation of a nation (nati... |
| geo_admin2 |
geographical admin level 2, the third large demarcation of a nation (nation =... |
| geo_admin3 |
geographical admin level 3, the third large demarcation of a nation (nation =... |
| gff_url |
a link to the where this genome's annotation file could be downloaded |
| haps |
a list of the microhaplotypes detected for this target |
| host_age |
if specimen is from a person, the age in years of the person, can be float va... |
| host_sex |
if specimen is from a person, the sex listed for that person |
| host_subject_id |
an identifier for the individual a specimen was collected from |
| host_taxon_id |
the NCBI taxonomy number of the host that the specimen was collected from |
| insert_location |
the intended genomic location of the insert of the amplicon (the location bet... |
| lat_lon |
the latitude and longitude of the collection site of the specimen |
| library_kit |
Name, version, and applicable cell or cycle numbers for the kit used to prepa... |
| library_layout |
Specify the configuration of reads, e |
| library_prep_plate_info |
plate location of where experiment was prepared for sequencing |
| library_screen |
Describe enrichment, screening, or normalization methods applied during ampli... |
| library_selection |
how amplification was done (common are PCR=Source material was selected by de... |
| library_source |
Source of amplification material (common names GENOMIC, TRANSCRIPTOMIC) |
| library_strategy |
what the nuceloacid sequencing/amplification strategy was (common names are A... |
| location |
what the intended genomic location of the primer is |
| marker_location |
the genomic location |
| markers_of_interest |
a list of covered markers of interest |
| masking |
masking info for the sequence |
| mhap_id |
the index for a microhaplotype for a target in the microhaplotypes_info list,... |
| mhap_location |
a genomic location that was analyzed for this target info, this allows listin... |
| mhaps_target_id |
the index for a target in the microhaplotypes_info list |
| microhaplotype_name |
an optional name for this microhaplotype |
| microhaplotypes |
a list of the microhaplotypes detected for a target |
| microhaplotypes_detected |
the microhaplotypes detected in this projects |
| microhaplotypes_info |
a list of the information on the representative microhaplotypes |
| microscopy_parasite_density_info |
one or more parasite densities in microliters for this specimen |
| name |
name of the genome |
| nucl_acid_amp |
Link to a reference or kit that describes the enzymatic amplification of nucl... |
| nucl_acid_amp_date |
the date of the nucleoacid amplification |
| nucl_acid_ext |
Link to a reference or kit that describes the recovery of nucleic acids from ... |
| nucl_acid_ext_date |
the date of the nucleoacid extraction |
| panel_id |
the index into the panel_info list |
| panel_info |
a list of info on the panels |
| panel_name |
a name for the panel |
| panel_targets |
a list of the target indexes in the target_info list |
| parasite_density |
the density in microliters |
| pcr_cond |
the method/conditions for PCR, List PCR cycles used to amplify the target |
| plate_col |
the column the specimen was in |
| plate_name |
a name of plate the specimen was in |
| plate_row |
the row the specimen was in |
| pmo_header |
the PMO information for this file including version etc |
| pmo_version |
the version of the PMO file, should be in the format of v[MAJOR] |
| program |
name of the program used for this portion of the pipeline |
| program_description |
a short description of what this method does |
| program_name |
the name of the program |
| program_version |
the version of generation method, should be in the format of v[MAJOR] |
| project_collector_chief_scientist |
can be collection of names separated by a semicolon if multiple people involv... |
| project_contributors |
a list of collaborators who contributed to this project |
| project_description |
a short description of the project |
| project_id |
the index into the project_info list |
| project_info |
the information about the projects stored in this PMO |
| project_name |
a name for the project, should be unique if multiple projects listed |
| project_type |
the type of project conducted, e |
| pseudocigar |
the pseudocigar of the haplotype |
| qpcr_parasite_density_info |
qpcr parasite density measurement |
| quality |
the ansi fastq per base quality score for this sequence, this is optional |
| reaction_name |
a name for this reaction |
| reactions |
a list of 1 or more reactions that this panel contains, each reactions list t... |
| read_count |
the read counts |
| read_counts_by_experimental_sample_by_stage |
a list by experiment_sample for the counts at each stage |
| read_counts_by_stage |
the read counts for different stages of the pipeline |
| read_counts_for_targets |
a list of counts by stage for a target |
| reads |
the read count associated with this microhaplotype |
| ref_seq |
the reference sequence of this genomic location |
| replacement_size |
the size of replacement mask |
| reverse_primer |
the reverse primer associated with this target |
| run_date |
the date when the run was done, should be YYYY-MM-DD |
| seq |
the DNA sequence |
| seq_center |
Name of facility where sequencing was performed (lab, core facility, or compa... |
| seq_date |
the date of sequencing, should be YYYY-MM or YYYY-MM-DD |
| seq_instrument_model |
the sequencing instrument model used to sequence the run, e |
| seq_platform |
the sequencing technology used to sequence the run, e |
| seq_segment_size |
the size of the masking |
| seq_start |
the start of the masking |
| sequencing_info |
a list of sequencing info for this project |
| sequencing_info_id |
the index into the sequencing_info list |
| sequencing_info_name |
a name of for the sequencing done, e |
| specimen_collect_device |
the way the specimen was collected, e |
| specimen_comments |
any additional comments about the specimen |
| specimen_id |
the index into the specimen_info list |
| specimen_info |
a list of all the specimens within this project |
| specimen_name |
an identifier for the specimen, should be unique within this sample set |
| specimen_store_loc |
the specimen store site, address or facility name |
| specimen_taxon_id |
the NCBI taxonomy number of the organism in specimen, can list multiple if a ... |
| specimen_type |
what type of specimen this is, e |
| stage |
the stage of the pipeline, e |
| stages |
the read counts by each stage |
| start |
the start of the location, 0-based positioning |
| storage_plate_info |
plate location of where specimen is stored if stored in a plate |
| strand |
which strand the location is, either + for plus strand or - for negative stra... |
| target_attributes |
a list of classification type for the primer target |
| target_id |
the index into the target_info list |
| target_info |
a list of info on the targets |
| target_name |
an identifier for this target |
| target_results |
a list of the microhaplotypes detected for a list of targets |
| targeted_genomes |
a list of genomes that the targets in TargetInfo refer to |
| targets |
a list of the microhaplotype for each targets |
| taxon_id |
the NCBI taxonomy number |
| total_raw_count |
the raw counts off the sequencing machine that a sample began with |
| travel_out_six_month |
Specification of the countries travelled in the last six months; can include ... |
| umis |
the unique molecular identifier (umi) count associated with this microhaploty... |
| url |
a link to the where this genome file could be downloaded |