| 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 samples |
| chrom |
the chromosome name |
| collection_country |
the name of country collected in, would be the same as admin level 0 |
| collection_date |
the date of the sample collection |
| collector |
the name of the primary person managing the specimen |
| demultiplexed_experiment_samples |
a list of the samples with the number of raw reads extracted |
| demultiplexed_targets |
a list of the targets extracted for a sample |
| 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 |
| end |
the end of the location, 0-based positioning |
| experiment_infos |
a list of experiments of all the seq/amp of samples within this project |
| experiment_sample_id |
a unique identifier for this sequence/amplification run on a specimen |
| experiment_samples |
a list of the microhaplotypes detected for a sample for various targets |
| forward_primers |
A list of forward primers associated with this target |
| gene_id |
an identifier of the gene, if any, is being covered with this targeted |
| 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 |
| host_taxon_id |
optional the NCBI taxonomy number of the host of the organism |
| individual_id |
an identifier for the individual a 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 |
| lib_kit |
Name, version, and applicable cell or cycle numbers for the kit used to prepa... |
| lib_layout |
Specify the configuration of reads, e |
| lib_screen |
Describe enrichment, screening, or normalization methods applied during ampli... |
| location |
what the intended genomic location of the primer is |
| masking |
masking info for the sequence |
| microhaplotype_id |
name of the microhaplotype, should be unique to this microhaplotype |
| microhaplotypes |
a list of the microhaplotypes detected for this target |
| microhaplotypes_detected |
the microhaplotypes detected in this projects |
| 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 nucleoacide 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 nucleoacide extraction |
| panel_id |
name of the panel |
| panel_info |
the info on the targeted sequencing panel used for this project |
| panel_targets |
a list of the target infos for the targets in this panel |
| parasite_density |
the parasite 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_name |
a name for this PMO, can be a concatenation of names if combined more than on... |
| population_clustering_method |
the method used to compare clustered/de-noised reads across samples for a tar... |
| postprocessing_bioinformatics_infos |
any additional methods that were applied to the processing of this file/analy... |
| program |
name of the program used for this portion of the pipeline |
| program_version |
versioning info for the program |
| project_name |
a name of the project under which the sample is organized |
| pseudocigar |
the pseudocigar of the haplotype |
| purpose |
the purpose for this method |
| quality |
the ansi fastq per base quality score for this sequence, this is optional |
| raw_read_count |
the raw read counts extracted for a target for a experiment sample |
| read_count |
the read count associated with this microhaplotype |
| ref_seq |
the reference sequence of this genomic location |
| replacement_size |
the size of replacement mask |
| representative_microhaplotype_id |
an identifier for the representative microhaplotype object collection |
| representative_microhaplotype_sequences |
a list of the representative sequences for the results for this project |
| reverse_primers |
A list of reverse primers associated with this target |
| samp_collect_device |
the way the sample was collected, e |
| samp_store_loc |
the sample store site, address or facility name |
| samp_taxon_id |
the NCBI taxonomy number of the organism of interest |
| sample_comments |
any additional comments about the sample |
| 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 |
the sequencing instrument used to sequence the run, e |
| seq_segment_size |
the size of the masking |
| seq_start |
the start of the masking |
| seqs |
a list of the microhaplotypes detected for a target |
| sequencing_info_id |
a unique identifier for this sequencing info |
| sequencing_infos |
the sequencing info for this project |
| specimen_id |
the name of the specimen of a individual |
| specimen_infos |
a list of SpecimenInfo of all the samples within this project |
| start |
the start of the location, 0-based positioning |
| strand |
which strand the location is, either + for plus strand or - for negative stra... |
| tar_amp_bioinformatics_info_id |
a unique identifier for this targeted amplicon bioinformatics pipeline run |
| taramp_bioinformatics_infos |
the bioinformatics pipeline/methods used to generated the amplicon analysis f... |
| target_demultiplexed_experiment_samples |
the raw demultiplex target counts for each sample |
| target_genome |
the info on the target reference genome for this panel |
| target_id |
name of the target |
| target_results |
a list of the microhaplotypes detected for a list of targets |
| target_type |
a list of classification type for the primer target |
| targets |
a list of the targets detected for this analysis |
| taxon_id |
the NCBI taxonomy number |
| umi_count |
the unique molecular identifier (umi) count associated with this microhaploty... |
| url |
a link to the where this genome file could be downloaded |
| version |
the genome version |