Table Names

This page provides a brief overview for each table within the Staphopia database. In order to save time, tables are described from the perspective of the database. For example instead of SNP (the Django model name), variant_snp the actual name in the database will be given. This will allow for easier construction of SQL statements.

Staphopia Tables

• Assembly

  • assembly_stats

• ENA Information

  • ena_experiment
  • ena_publication
  • ena_run
  • ena_study
  • ena_tosample

• Gene Information (Annotations)

  • gene_clustermembers
  • gene_clusters
  • gene_contigs
  • gene_features
  • gene_names
  • gene_organism
  • gene_references

• K-mers

  • kmer_binary
  • kmer_count
  • kmer_total

• MLST

  • mlst_blast
  • mlst_sequencetypes
  • mlst_srst2

• Sample Information

  • sample_metadata
  • sample_pipeline
  • sample_upload

• Sequence Quality

  • sequence_quality

• Variant (SNP/InDel Calls)

  • variant_annotation
  • variant_comment
  • variant_confidence
  • variant_counts
  • variant_snpcounts
  • variant_filter
  • variant_indel
  • variant_reference
  • variant_snp
  • variant_toindel
  • variant_tosnp

Assembly

assembly_stats

        Column            |     Type     |                          Modifiers                          | Storage |

------------------------------|--------------|-------------------------------------------------------------|---------| id | integer | not null default nextval('assembly_stats_id_seq'::regclass) | plain | is_scaffolds | boolean | not null | plain | total_contig | smallint | not null | plain | total_contig_length | integer | not null | plain | min_contig_length | integer | not null | plain | median_contig_length | integer | not null | plain | mean_contig_length | numeric(9,2) | not null | main | max_contig_length | integer | not null | plain | n50_contig_length | integer | not null | plain | l50_contig_count | smallint | not null | plain | ng50_contig_length | integer | not null | plain | lg50_contig_count | smallint | not null | plain | contigs_greater_1k | smallint | not null | plain | contigs_greater_10k | smallint | not null | plain | contigs_greater_100k | smallint | not null | plain | contigs_greater_1m | smallint | not null | plain | percent_contigs_greater_1k | numeric(4,2) | not null | main | percent_contigs_greater_10k | numeric(4,2) | not null | main | percent_contigs_greater_100k | numeric(4,2) | not null | main | percent_contigs_greater_1m | numeric(4,2) | not null | main | contig_percent_a | numeric(4,2) | not null | main | contig_percent_t | numeric(4,2) | not null | main | contig_percent_g | numeric(4,2) | not null | main | contig_percent_c | numeric(4,2) | not null | main | contig_percent_n | numeric(4,2) | not null | main | contig_non_acgtn | numeric(4,2) | not null | main | num_contig_non_acgtn | smallint | not null | plain | sample_id | integer | not null | plain |

Indexes:
    "assembly_stats_pkey" PRIMARY KEY, btree (id)
    "assembly_stats_sample_id_2701b767476a61b7_uniq" UNIQUE CONSTRAINT, btree (sample_id, is_scaffolds)
    "assembly_stats_2242a234" btree (is_scaffolds)
    "assembly_stats_c09c8085" btree (sample_id)

ENA

ena_experiment

       Column           | Type | Modifiers | Storage  |

----------------------------|------|-----------|----------| experiment_accession | text | not null | extended | experiment_title | text | not null | extended | experiment_alias | text | not null | extended | sample_accession | text | not null | extended | secondary_sample_accession | text | not null | extended | submission_accession | text | not null | extended | tax_id | text | not null | extended | scientific_name | text | not null | extended | instrument_platform | text | not null | extended | instrument_model | text | not null | extended | library_layout | text | not null | extended | library_strategy | text | not null | extended | library_selection | text | not null | extended | center_name | text | not null | extended | study_accession | text | not null | extended |

Indexes:
    "ena_experiment_pkey" PRIMARY KEY, btree (experiment_accession)
    "ena_experiment_6a0c5df2" btree (instrument_platform)
    "ena_experiment_8cd0a95d" btree (study_accession)
    "ena_experiment_experiment_accession_78e80ad55e7e5209_like" btree (experiment_accession text_pattern_ops)
    "ena_experiment_instrument_platform_7826b6971eb893db_like" btree (instrument_platform text_pattern_ops)

ena_publication

    Column        |  Type   |                          Modifiers                           | Storage  |

----------------------|---------|--------------------------------------------------------------|----------| id | integer | not null default nextval('ena_publication_id_seq'::regclass) | plain | pmid | text | not null | extended | experiment_accession | text | not null | extended |

Indexes:
    "ena_publication_pkey" PRIMARY KEY, btree (id)
    "ena_publication_experiment_accession_36f9435cdb3ab754_uniq" UNIQUE CONSTRAINT, btree (experiment_accession, pmid)
    "ena_publication_c4f15a54" btree (experiment_accession)
    "ena_publication_experiment_accession_77abbd3c8c8dae5b_like" btree (experiment_accession text_pattern_ops)

ena_run

    Column        |     Type      | Modifiers | Storage  |

----------------------|---------------|-----------|----------| run_accession | text | not null | extended | is_paired | boolean | not null | plain | run_alias | text | not null | extended | read_count | bigint | not null | plain | base_count | bigint | not null | plain | mean_read_length | numeric(10,2) | not null | main | coverage | numeric(10,2) | not null | main | first_public | text | not null | extended | fastq_bytes | text | not null | extended | fastq_md5 | text | not null | extended | fastq_aspera | text | not null | extended | fastq_ftp | text | not null | extended | experiment_accession | text | not null | extended |

Indexes:
    "ena_run_pkey" PRIMARY KEY, btree (run_accession)
    "ena_run_c4f15a54" btree (experiment_accession)
    "ena_run_experiment_accession_292794787d933064_like" btree (experiment_accession text_pattern_ops)
    "ena_run_run_accession_3325d003c60f8137_like" btree (run_accession text_pattern_ops)

ena_study

      Column           | Type | Modifiers | Storage  |

---------------------------|------|-----------|----------| study_accession | text | not null | extended | secondary_study_accession | text | not null | extended | study_title | text | not null | extended | study_alias | text | not null | extended |

Indexes:
    "ena_study_pkey" PRIMARY KEY, btree (study_accession)
    "ena_study_study_accession_607a0e827f9b141d_like" btree (study_accession text_pattern_ops)

ena_tosample

    Column        |  Type   |                         Modifiers                         | Storage  |

----------------------|---------|-----------------------------------------------------------|----------| id | integer | not null default nextval('ena_tosample_id_seq'::regclass) | plain | experiment_accession | text | not null | extended | sample_id | integer | not null | plain |

Indexes:
    "ena_tosample_pkey" PRIMARY KEY, btree (id)
    "ena_tosample_experiment_accession_1bd15d0ef3d7f0e1_uniq" UNIQUE CONSTRAINT, btree (experiment_accession, sample_id)
    "ena_tosample_c09c8085" btree (sample_id)
    "ena_tosample_c4f15a54" btree (experiment_accession)
    "ena_tosample_experiment_accession_3656e834d439ae9f_like" btree (experiment_accession text_pattern_ops)

Annotation

gene_clustermembers

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_clustermembers_id_seq'::regclass)	plain
member	text	not null	extended
entry_name	text	not null	extended
length	integer	not null	plain
is_rep	boolean	not null	plain
is_seed	boolean	not null	plain
cluster_id	integer	not null	plain
gene_id	integer	not null	plain
organism_id	integer	not null	plain
protein_id	integer	not null	plain

Indexes:
    "gene_clustermembers_pkey" PRIMARY KEY, btree (id)
    "gene_clustermembers_member_key" UNIQUE CONSTRAINT, btree (member)
    "gene_clustermembers_2bf283a7" btree (organism_id)
    "gene_clustermembers_4ff9f3a6" btree (protein_id)
    "gene_clustermembers_6c57aa00" btree (gene_id)
    "gene_clustermembers_a97b1c12" btree (cluster_id)
    "gene_clustermembers_member_2dc472e1ea5b1a21_like" btree (member text_pattern_ops)

gene_clusters

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_clusters_id_seq'::regclass)	plain
name	text	not null	extended
aa	text	not null	extended

Indexes:
    "gene_clusters_pkey" PRIMARY KEY, btree (id)
    "gene_clusters_name_key" UNIQUE CONSTRAINT, btree (name)
    "gene_clusters_name_3fc4e1fe22fcccca_like" btree (name text_pattern_ops)

gene_contigs

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_contigs_id_seq'::regclass)	plain
name	text	not null	extended
sequence	text	not null	extended
sample_id	integer	not null	plain

Indexes:
    "gene_contigs_pkey" PRIMARY KEY, btree (id)
    "gene_contigs_sample_id_78af5785299a980d_uniq" UNIQUE CONSTRAINT, btree (sample_id, name)
    "gene_contigs_b068931c" btree (name)
    "gene_contigs_c09c8085" btree (sample_id)
    "gene_contigs_name_2a6dbe9155b0f4fb_like" btree (name text_pattern_ops)

gene_features

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_features_id_seq'::regclass)	plain
start	integer	not null	plain
end	integer	not null	plain
is_positive	boolean	not null	plain
is_tRNA	boolean	not null	plain
phase	smallint	not null	plain
dna	text	not null	extended
aa	text	not null	extended
cluster_id	integer	not null	plain
contig_id	integer	not null	plain
sample_id	integer	not null	plain

Indexes:
    "gene_features_pkey" PRIMARY KEY, btree (id)
    "gene_features_sample_id_2d59ee91e76f3b20_uniq" UNIQUE CONSTRAINT, btree (sample_id, contig_id, cluster_id, start, "end")
    "gene_features_a97b1c12" btree (cluster_id)
    "gene_features_c09c8085" btree (sample_id)
    "gene_features_c90fc43a" btree (contig_id)

gene_names

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_names_id_seq'::regclass)	plain
name	text	not null	extended

Indexes:
    "gene_names_pkey" PRIMARY KEY, btree (id)

gene_organism

Column	Type	Modifiers	Storage
id	integer	not null default nextval('gene_organism_id_seq'::regclass)	plain
taxon_id	integer	not null	plain
name	text	not null	extended

Indexes: "gene_organism_pkey" PRIMARY KEY, btree (id)

gene_references

Column     |  Type   |                          Modifiers                           | Storage  |

---------------|---------|--------------------------------------------------------------|----------| id | integer | not null default nextval('gene_references_id_seq'::regclass) | plain | dna | text | not null | extended | aa | text | not null | extended | annotation_id | integer | not null | plain | cluster_id | integer | not null | plain | reference_id | integer | not null | plain | end | integer | not null | plain | is_positive | boolean | not null | plain | is_tRNA | boolean | not null | plain | start | integer | not null | plain |

Indexes:
    "gene_references_pkey" PRIMARY KEY, btree (id)
    "gene_references_10d1a950" btree (reference_id)
    "gene_references_a97b1c12" btree (cluster_id)
    "gene_references_e70a1874" btree (annotation_id)

K-mers

kmer_binary

Column	Type	Modifiers	Storage
id	integer	not null default nextval('kmer_binary_id_seq'::regclass)	plain
string	bytea	not null	extended

Indexes:
    "kmer_binary_pkey" PRIMARY KEY, btree (id)
    "kmer_binary_string_key" UNIQUE CONSTRAINT, btree (string)

kmer_count

Column	Type	Modifiers	Storage
id	integer	not null default nextval('kmer_count_id_seq'::regclass)	plain
count	integer	not null	plain
sample_id	integer	not null	plain
string_id	integer	not null	plain

Indexes:
    "kmer_count_pkey" PRIMARY KEY, btree (id)
    "kmer_count_sample_id_3851872189dfeb40_uniq" UNIQUE CONSTRAINT, btree (sample_id, string_id)
    "kmer_count_c09c8085" btree (sample_id)
    "kmer_count_fa206039" btree (string_id)

kmer_total"

Column	Type	Modifiers	Storage
id	integer	not null default nextval('kmer_total_id_seq'::regclass)	plain
total	integer	not null	plain
singletons	integer	not null	plain
new_kmers	integer	not null	plain
runtime	integer	not null	plain
sample_id	integer	not null	plain

Indexes:
    "kmer_total_pkey" PRIMARY KEY, btree (id)
    "kmer_total_c09c8085" btree (sample_id)

MLST

mlst_blast

Column	Type	Modifiers	Storage
id	integer	not null default nextval('mlst_blast_id_seq'::regclass)	plain
locus_name	character varying(4)	not null	extended
locus_id	smallint	not null	plain
bitscore	smallint	not null	plain
slen	smallint	not null	plain
length	smallint	not null	plain
gaps	smallint	not null	plain
mismatch	smallint	not null	plain
pident	numeric(5,2)	not null	main
evalue	numeric(7,2)	not null	main
sample_id	integer	not null	plain

Indexes:
    "mlst_blast_pkey" PRIMARY KEY, btree (id)
    "mlst_blast_sample_id_15f1e0f68e36debb_uniq" UNIQUE CONSTRAINT, btree (sample_id, locus_name, locus_id)
    "mlst_blast_c09c8085" btree (sample_id)

mlst_sequencetypes

Column    |           Type           |                            Modifiers                            | Storage |

--------------|--------------------------|-----------------------------------------------------------------|---------| id | integer | not null default nextval('mlst_sequencetypes_id_seq'::regclass) | plain | st | integer | not null | plain | arcc | integer | not null | plain | aroe | integer | not null | plain | glpf | integer | not null | plain | gmk | integer | not null | plain | pta | integer | not null | plain | tpi | integer | not null | plain | yqil | integer | not null | plain | last_updated | timestamp with time zone | not null | plain |

Indexes:
    "mlst_sequencetypes_pkey" PRIMARY KEY, btree (id)
    "mlst_sequencetypes_ST_key" UNIQUE CONSTRAINT, btree ("ST")

mlst_srst2

Column	Type	Modifiers	Storage
id	integer	not null default nextval('mlst_srst2_id_seq'::regclass)	plain
st_original	text	not null	extended
st_stripped	integer	not null	plain
is_exact	boolean	not null	plain
arcc	text	not null	extended
aroe	text	not null	extended
glpf	text	not null	extended
gmk	text	not null	extended
pta	text	not null	extended
tpi	text	not null	extended
yqil	text	not null	extended
mismatches	text	not null	extended
uncertainty	text	not null	extended
depth	numeric(8,3)	not null	main
maxMAF	numeric(11,7)	not null	main
sample_id	integer	not null	plain

Indexes:
    "mlst_srst2_pkey" PRIMARY KEY, btree (id)
    "mlst_srst2_sample_id_key" UNIQUE CONSTRAINT, btree (sample_id)
    "mlst_srst2_1bd961ca" btree (st_stripped)
    "mlst_srst2_1ab40400" btree (is_exact)

Sample Information

sample_metadata

      Column           |          Type          |                          Modifiers                           | Storage  |

---------------------------|------------------------|--------------------------------------------------------------|----------| id | integer | not null default nextval('sample_metadata_id_seq'::regclass) | plain | sample_tag | text | not null | extended | contact_name | text | not null | extended | contact_email | character varying(254) | not null | extended | contact_link | character varying(200) | not null | extended | sequencing_center | text | not null | extended | sequencing_center_link | character varying(200) | not null | extended | sequencing_date | date | not null | plain | sequencing_libaray_method | text | not null | extended | sequencing_platform | text | not null | extended | publication_link | character varying(200) | not null | extended | pubmed_id | text | not null | extended | doi | text | not null | extended | funding_agency | text | not null | extended | funding_agency_link | character varying(200) | not null | extended | strain | text | not null | extended | isolation_date | date | not null | plain | isolation_country | text | not null | extended | isolation_city | text | not null | extended | isolation_region | text | not null | extended | host_name | text | not null | extended | host_health | text | not null | extended | host_age | smallint | not null | plain | host_gender | text | not null | extended | comments | text | not null | extended | vancomycin_mic | numeric(6,3) | not null | main | penicillin_mic | numeric(6,3) | not null | main | oxacillin_mic | numeric(6,3) | not null | main | clindamycin_mic | numeric(6,3) | not null | main | daptomycin_mic | numeric(6,3) | not null | main | levofloxacin_mic | numeric(6,3) | not null | main | linezolid_mic | numeric(6,3) | not null | main | rifampin_mic | numeric(6,3) | not null | main | tetracycline_mic | numeric(6,3) | not null | main | trimethoprim_mic | numeric(6,3) | not null | main | source | text | not null | extended | is_public | boolean | not null | plain | is_paired | boolean | not null | plain | is_published | boolean | not null | plain | user_id | integer | not null | plain |

Indexes:
    "sample_metadata_pkey" PRIMARY KEY, btree (id)
    "sample_metadata_11725655" btree (is_public)
    "sample_metadata_75892900" btree (is_published)
    "sample_metadata_b3fa01dd" btree (sample_tag)
    "sample_metadata_e8701ad4" btree (user_id)
    "sample_metadata_sample_tag_329e6fe76c09a51f_like" btree (sample_tag text_pattern_ops)

sample_pipeline

Column	Type	Modifiers	Storage
id	integer	not null default nextval('sample_pipeline_id_seq'::regclass)	plain
assembly	text	not null	extended
gene	text	not null	extended
kmer	text	not null	extended
mlst	text	not null	extended
sequence	text	not null	extended
variant	text	not null	extended
sample_id	integer	not null	plain

Indexes:
    "sample_pipeline_pkey" PRIMARY KEY, btree (id)
    "sample_pipeline_sample_id_key" UNIQUE CONSTRAINT, btree (sample_id)

sample_upload

Column	Type	Modifiers	Storage
sample_id	integer	not null	plain
path	character varying(100)	not null	extended
md5sum	character varying(32)	not null	extended

Indexes:
    "sample_upload_pkey" PRIMARY KEY, btree (sample_id)
    "sample_upload_md5sum_key" UNIQUE CONSTRAINT, btree (md5sum)
    "sample_upload_md5sum_4c1e5476f2ea753_like" btree (md5sum varchar_pattern_ops)

Sequence Quality

sequence_quality

  Column      |     Type      |                           Modifiers                           | Storage |

------------------|---------------|---------------------------------------------------------------|---------| id | integer | not null default nextval('sequence_quality_id_seq'::regclass) | plain | is_original | boolean | not null | plain | rank | smallint | not null | plain | total_bp | bigint | not null | plain | total_reads | bigint | not null | plain | coverage | numeric(7,2) | not null | main | min_read_length | integer | not null | plain | mean_read_length | numeric(10,3) | not null | main | max_read_length | integer | not null | plain | qual_mean | numeric(6,3) | not null | main | qual_std | numeric(6,3) | not null | main | qual_25th | numeric(6,3) | not null | main | qual_median | numeric(6,3) | not null | main | qual_75th | numeric(6,3) | not null | main | sample_id | integer | not null | plain |

Indexes:
    "sequence_quality_pkey" PRIMARY KEY, btree (id)
    "sequence_quality_sample_id_2748bdad20282c51_uniq" UNIQUE CONSTRAINT, btree (sample_id, is_original)
    "sequence_quality_3d0351e8" btree (is_original)
    "sequence_quality_65dc5d2a" btree (rank)
    "sequence_quality_c09c8085" btree (sample_id)

Variant (SNP/InDel) Calling

variant_annotation

Column    |         Type          |                            Modifiers                            | Storage  |

--------------|-----------------------|-----------------------------------------------------------------|----------| id | integer | not null default nextval('variant_annotation_id_seq'::regclass) | plain | locus_tag | character varying(24) | not null | extended | protein_id | character varying(24) | not null | extended | gene | character varying(12) | not null | extended | db_xref | text | not null | extended | product | text | not null | extended | note | text | not null | extended | reference_id | integer | not null | plain |

Indexes:
    "variant_annotation_pkey" PRIMARY KEY, btree (id)
    "variant_annotation_10d1a950" btree (reference_id)

variant_comment

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_comment_id_seq'::regclass)	plain
comment	text	not null	extended

Indexes:
    "variant_comment_pkey" PRIMARY KEY, btree (id)
    "variant_comment_comment_key" UNIQUE CONSTRAINT, btree (comment)
    "variant_comment_comment_767f0ad1828fdabf_like" btree (comment text_pattern_ops)

variant_confidence

   Column       |     Type     |                            Modifiers                            | Storage  |

--------------------|--------------|-----------------------------------------------------------------|----------| id | integer | not null default nextval('variant_confidence_id_seq'::regclass) | plain | AC | text | not null | extended | AD | text | not null | extended | AF | numeric(8,3) | not null | main | DP | integer | not null | plain | GQ | integer | not null | plain | GT | text | not null | extended | MQ | numeric(8,3) | not null | main | PL | text | not null | extended | QD | numeric(8,3) | not null | main | quality | numeric(8,3) | not null | main | reference_position | integer | not null | plain | sample_id | integer | not null | plain |

Indexes:
    "variant_confidence_pkey" PRIMARY KEY, btree (id)
    "variant_confidence_c09c8085" btree (sample_id)

variant_counts

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_counts_id_seq'::regclass)	plain
snp	integer	not null	plain
indel	integer	not null	plain
confidence	integer	not null	plain
sample_id	integer	not null	plain

Indexes:
    "variant_counts_pkey" PRIMARY KEY, btree (id)
    "variant_counts_c09c8085" btree (sample_id)

variant_filter

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_filter_id_seq'::regclass)	plain
name	text	not null	extended

Indexes:
    "variant_filter_pkey" PRIMARY KEY, btree (id)
    "variant_filter_name_key" UNIQUE CONSTRAINT, btree (name)
    "variant_filter_name_400bafac6f2822a6_like" btree (name text_pattern_ops)

variant_snpcounts

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_snpcounts_id_seq'::regclass)	plain
count	integer	not null	plain
snp_id	integer	not null	plain

Indexes:
    "variant_snpcounts_pkey" PRIMARY KEY, btree (id)
    "variant_snpcounts_c57207ae" btree (snp_id)
    "variant_snpcounts_e2942a04" btree (count)

variant_indel

   Column       |  Type   |                         Modifiers                          | Storage  |

--------------------|---------|------------------------------------------------------------|----------| id | integer | not null default nextval('variant_indel_id_seq'::regclass) | plain | reference_position | integer | not null | plain | reference_base | text | not null | extended | alternate_base | text | not null | extended | is_deletion | boolean | not null | plain | annotation_id | integer | not null | plain | reference_id | integer | not null | plain |

Indexes:
    "variant_indel_pkey" PRIMARY KEY, btree (id)
    "variant_indel_reference_id_547a401e880b518c_uniq" UNIQUE CONSTRAINT, btree (reference_id, reference_position, reference_base, alternate_base)
    "variant_indel_10d1a950" btree (reference_id)
    "variant_indel_1c86ae80" btree (reference_position)
    "variant_indel_6c00cd75" btree (is_deletion)
    "variant_indel_e70a1874" btree (annotation_id)

variant_reference

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_reference_id_seq'::regclass)	plain
name	text	not null	extended

Indexes:
        "variant_reference_pkey" PRIMARY KEY, btree (id)
        "variant_reference_name_key" UNIQUE CONSTRAINT, btree (name)
        "variant_reference_name_481c1fbe9b67c108_like" btree (name text_pattern_ops)

variant_snp

    Column        |         Type         |                        Modifiers                         | Storage  |

----------------------|----------------------|----------------------------------------------------------|----------| id | integer | not null default nextval('variant_snp_id_seq'::regclass) | plain | reference_position | integer | not null | plain | reference_base | character varying(1) | not null | extended | alternate_base | character varying(1) | not null | extended | reference_codon | character varying(3) | not null | extended | alternate_codon | character varying(3) | not null | extended | reference_amino_acid | character varying(1) | not null | extended | alternate_amino_acid | character varying(1) | not null | extended | codon_position | integer | not null | plain | snp_codon_position | smallint | not null | plain | amino_acid_change | text | not null | extended | is_synonymous | smallint | not null | plain | is_transition | smallint | not null | plain | is_genic | smallint | not null | plain | annotation_id | integer | not null | plain | reference_id | integer | not null | plain |

Indexes:
        "variant_snp_pkey" PRIMARY KEY, btree (id)
        "variant_snp_reference_id_7a69b43c78491f2b_uniq" UNIQUE CONSTRAINT, btree (reference_id, reference_position, reference_base, alternate_base)
        "variant_snp_10d1a950" btree (reference_id)
        "variant_snp_1c86ae80" btree (reference_position)
        "variant_snp_e70a1874" btree (annotation_id)

variant_toindel

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_toindel_id_seq'::regclass)	plain
filters_id	integer	not null	plain
indel_id	integer	not null	plain
sample_id	integer	not null	plain

Indexes:
        "variant_toindel_pkey" PRIMARY KEY, btree (id)
        "variant_toindel_sample_id_ebbe8d32d6f85fb_uniq" UNIQUE CONSTRAINT, btree (sample_id, indel_id)
        "variant_toindel_6628046e" btree (filters_id)
        "variant_toindel_c09c8085" btree (sample_id)
        "variant_toindel_f8c5f21f" btree (indel_id)

variant_tosnp

Column	Type	Modifiers	Storage
id	integer	not null default nextval('variant_tosnp_id_seq'::regclass)	plain
comment_id	integer	not null	plain
filters_id	integer	not null	plain
sample_id	integer	not null	plain
snp_id	integer	not null	plain

Indexes:
        "variant_tosnp_pkey" PRIMARY KEY, btree (id)
        "variant_tosnp_sample_id_2d8402c0fb24b75_uniq" UNIQUE CONSTRAINT, btree (sample_id, snp_id)
        "variant_tosnp_6628046e" btree (filters_id)
        "variant_tosnp_69b97d17" btree (comment_id)
        "variant_tosnp_c09c8085" btree (sample_id)
        "variant_tosnp_c57207ae" btree (snp_id)