diff test-data/rif_resistant.results.json @ 3:42818629ec4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents 02d81b994ef5
children
line wrap: on
line diff
--- a/test-data/rif_resistant.results.json	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant.results.json	Fri May 31 20:06:49 2024 +0000
@@ -1,1 +1,704 @@
-{"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], ["Chromosome", 763409], ["Chromosome", 763410], ["Chromosome", 763411], ["Chromosome", 763412], ["Chromosome", 763413], ["Chromosome", 763414], ["Chromosome", 763415], ["Chromosome", 763416], ["Chromosome", 763417], ["Chromosome", 763418], ["Chromosome", 763419], ["Chromosome", 763420], ["Chromosome", 1834082], ["Chromosome", 1834083], ["Chromosome", 1834084], ["Chromosome", 1834085], ["Chromosome", 1834086], ["Chromosome", 1834087], ["Chromosome", 1834088], ["Chromosome", 1834089], ["Chromosome", 1834090], ["Chromosome", 1834091], ["Chromosome", 1834092], ["Chromosome", 1834093], ["Chromosome", 1834094], ["Chromosome", 1834095], ["Chromosome", 1834251], ["Chromosome", 1834252], ["Chromosome", 1834253], ["Chromosome", 1834254], ["Chromosome", 1834255], ["Chromosome", 1834256], ["Chromosome", 1834257], ["Chromosome", 1834258], ["Chromosome", 1834259], ["Chromosome", 1834260], ["Chromosome", 1834261], ["Chromosome", 1834262], ["Chromosome", 1834263], ["Chromosome", 1834264], ["Chromosome", 1834265], ["Chromosome", 1834266], ["Chromosome", 1834267], ["Chromosome", 1834268], ["Chromosome", 1834269], ["Chromosome", 1834270], ["Chromosome", 1834271], ["Chromosome", 1834272], ["Chromosome", 1834273], ["Chromosome", 4245997], ["Chromosome", 4245998], ["Chromosome", 4245999], ["Chromosome", 4246000], ["Chromosome", 4246001], ["Chromosome", 4246002], ["Chromosome", 4246003], ["Chromosome", 4246004], ["Chromosome", 4246005], ["Chromosome", 4246006], ["Chromosome", 4246007], ["Chromosome", 4246008], ["Chromosome", 4246009], ["Chromosome", 4246010], ["Chromosome", 4246011], ["Chromosome", 4246012], ["Chromosome", 4246155], ["Chromosome", 4246156], ["Chromosome", 4246157], ["Chromosome", 4246158], ["Chromosome", 4246159], ["Chromosome", 4246160], ["Chromosome", 4246161], ["Chromosome", 4246162], ["Chromosome", 4246163], ["Chromosome", 4246164], ["Chromosome", 4246165], ["Chromosome", 4246166], ["Chromosome", 4246167], ["Chromosome", 4246168], ["Chromosome", 4246169], ["Chromosome", 4246170], ["Chromosome", 4246171], ["Chromosome", 4246172], ["Chromosome", 4246173], ["Chromosome", 4246174], ["Chromosome", 4246175], ["Chromosome", 4246176], ["Chromosome", 4246177], ["Chromosome", 4246178], ["Chromosome", 4246179], ["Chromosome", 4246180], ["Chromosome", 4246181], ["Chromosome", 4246182], ["Chromosome", 4246183], ["Chromosome", 4246184], ["Chromosome", 4248018], ["Chromosome", 4248019], ["Chromosome", 4248020], ["Chromosome", 4248021], ["Chromosome", 4248022], ["Chromosome", 4248023], ["Chromosome", 4248024], ["Chromosome", 4248025], ["Chromosome", 4248026], ["Chromosome", 4248027], ["Chromosome", 4248028], ["Chromosome", 4248029], ["Chromosome", 4248030], ["Chromosome", 4248031], ["Chromosome", 4248032], ["Chromosome", 4248033], ["Chromosome", 4248034], ["Chromosome", 4248035], ["Chromosome", 4248036], ["Chromosome", 4248037], ["Chromosome", 4248038], ["Chromosome", 4248039], ["Chromosome", 4248040], ["Chromosome", 4248041], ["Chromosome", 4248042], ["Chromosome", 4248043], ["Chromosome", 4248044], ["Chromosome", 4248045], ["Chromosome", 4248046], ["Chromosome", 4248047], ["Chromosome", 4248184], ["Chromosome", 4248185], ["Chromosome", 4248186], ["Chromosome", 4248187], ["Chromosome", 4248188], ["Chromosome", 4248189], ["Chromosome", 4248190], ["Chromosome", 4248191], ["Chromosome", 4248192], ["Chromosome", 4248193], ["Chromosome", 4248194], ["Chromosome", 4248195], ["Chromosome", 4248196], ["Chromosome", 4248197], ["Chromosome", 4248198], ["Chromosome", 4248199], ["Chromosome", 4248200], ["Chromosome", 4248201], ["Chromosome", 4248202], ["Chromosome", 4248203], ["Chromosome", 4248204], ["Chromosome", 4248205], ["Chromosome", 4248206], ["Chromosome", 4248207], ["Chromosome", 4248208], ["Chromosome", 4248209], ["Chromosome", 4248210], ["Chromosome", 4248211], ["Chromosome", 4248212], ["Chromosome", 4248213], ["Chromosome", 4248214], ["Chromosome", 4248215]], "qc": {"pct_reads_mapped": 87.21, "num_reads_mapped": 5515}, "missing_regions": {"Rv0005": 1.0, "Rv0006": 1.0, "Rv0667": 0.0, "Rv0668": 0.9804707060590886, "Rv0678": 1.0, "Rv0682": 1.0, "Rv0701": 1.0, "Rv1267c": 1.0, "rrs": 1.0, "rrl": 1.0, "Rv1483": 1.0, "Rv1484": 1.0, "Rv1630": 0.9029247044181705, "Rv1694": 1.0, "Rv1908c": 1.0, "Rv2043c": 1.0, "Rv2245": 1.0, "Rv2416c": 1.0, "Rv2428": 1.0, "Rv2447c": 1.0, "Rv2671": 1.0, "Rv2754c": 1.0, "Rv2764c": 1.0, "Rv2780": 1.0, "Rv3261": 1.0, "Rv3423c": 1.0, "Rv3601c": 1.0, "Rv3793": 1.0, "Rv3794": 0.9575037147102526, "Rv3795": 0.9584344660194175, "Rv3854c": 1.0, "Rv3855": 1.0, "Rv3919c": 1.0}, "lineage": [{"lin": "lineage2", "family": "East-Asian", "spoligotype": "Beijing", "rd": "RD105", "frac": 1.0}, {"lin": "lineage2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD207", "rd": "RD105;RD207", "frac": 1.0}, {"lin": "lineage2.2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD105/RD207", "rd": "RD105;RD207", "frac": 1.0}], "main_lin": "lineage2", "sublin": "lineage2.2.2", "dr_variants": [{"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 761110, "type": "missense", "change": "p.Asp435Val", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "435D>435V", "drug": "rifampicin"}], "other_variants": [{"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 763031, "type": "synonymous", "change": "c.3225T>C", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "3225T>C"}, {"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 1834177, "type": "synonymous", "change": "c.636A>C", "freq": 1.0, "locus_tag": "Rv1630", "gene": "rpsA", "_internal_change": "636A>C"}], "XDR": "", "MDR": "", "drtype": "Drug-resistant", "id": "rif_resistant", "tbprofiler_version": "2.1.0", "pipeline": {"mapper": "bwa", "variant_caller": "BCFtools"}}
\ No newline at end of file
+{
+    "id": "tbprofiler",
+    "timestamp": "2024-05-31T15:43:38.437239",
+    "pipeline": {
+        "software_version": "6.2.1",
+        "db_version": {
+            "name": "tbdb",
+            "commit": "82777ea",
+            "Author": "Jody Phelan <jody.phelan@lshtm.ac.uk>",
+            "Date": "Sun Mar 17 01:14:00 2024 +0000"
+        },
+        "software": [
+            {
+                "process": "variant_calling",
+                "software": "freebayes"
+            },
+            {
+                "process": "depth_calculation",
+                "software": "samtools"
+            }
+        ]
+    },
+    "notes": [],
+    "lineage": [
+        {
+            "fraction": 1.0,
+            "lineage": "lineage2.2.2",
+            "family": "East-Asian (Beijing)",
+            "rd": "RD105;RD207",
+            "support": [
+                {
+                    "id": "lineage2.2.2",
+                    "chrom": "Chromosome",
+                    "pos": 154990,
+                    "target_allele_count": 47,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2.2.2",
+                    "chrom": "Chromosome",
+                    "pos": 346693,
+                    "target_allele_count": 23,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2.2.2",
+                    "chrom": "Chromosome",
+                    "pos": 449194,
+                    "target_allele_count": 22,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2.2.2",
+                    "chrom": "Chromosome",
+                    "pos": 1565566,
+                    "target_allele_count": 46,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2.2.2",
+                    "chrom": "Chromosome",
+                    "pos": 2640807,
+                    "target_allele_count": 49,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                }
+            ]
+        },
+        {
+            "fraction": 0.9940119760479041,
+            "lineage": "lineage2",
+            "family": "East-Asian",
+            "rd": "RD105",
+            "support": [
+                {
+                    "id": "lineage2",
+                    "chrom": "Chromosome",
+                    "pos": 497491,
+                    "target_allele_count": 64,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2",
+                    "chrom": "Chromosome",
+                    "pos": 811753,
+                    "target_allele_count": 51,
+                    "other_allele_count": 1,
+                    "target_allele_percent": 98.07692307692307
+                },
+                {
+                    "id": "lineage2",
+                    "chrom": "Chromosome",
+                    "pos": 4254431,
+                    "target_allele_count": 51,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                }
+            ]
+        },
+        {
+            "fraction": 1.0,
+            "lineage": "lineage2.2",
+            "family": "East-Asian (Beijing)",
+            "rd": "RD105;RD207",
+            "support": [
+                {
+                    "id": "lineage2.2",
+                    "chrom": "Chromosome",
+                    "pos": 1849051,
+                    "target_allele_count": 77,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                },
+                {
+                    "id": "lineage2.2",
+                    "chrom": "Chromosome",
+                    "pos": 2505085,
+                    "target_allele_count": 36,
+                    "other_allele_count": 0,
+                    "target_allele_percent": 100.0
+                }
+            ]
+        }
+    ],
+    "main_lineage": "lineage2",
+    "sub_lineage": "lineage2.2.2",
+    "spoligotype": null,
+    "drtype": "RR-TB",
+    "dr_variants": [
+        {
+            "chrom": "Chromosome",
+            "pos": 761110,
+            "ref": "A",
+            "alt": "T",
+            "depth": 43,
+            "freq": 1.0,
+            "sv": false,
+            "filter": "pass",
+            "forward_reads": 20,
+            "reverse_reads": 23,
+            "sv_len": null,
+            "gene_id": "Rv0667",
+            "gene_name": "rpoB",
+            "feature_id": "CCP43410",
+            "type": "missense_variant",
+            "change": "p.Asp435Val",
+            "nucleotide_change": "c.1304A>T",
+            "protein_change": "p.Asp435Val",
+            "annotation": [
+                {
+                    "type": "drug_resistance",
+                    "drug": "rifampicin",
+                    "original_mutation": "p.Asp435Val",
+                    "confidence": "Assoc w R",
+                    "source": "WHO catalogue v2",
+                    "comment": ""
+                }
+            ],
+            "consequences": [
+                {
+                    "gene_id": "Rv0667",
+                    "gene_name": "rpoB",
+                    "feature_id": "CCP43410",
+                    "type": "missense_variant",
+                    "nucleotide_change": "c.1304A>T",
+                    "protein_change": "p.Asp435Val",
+                    "annotation": [
+                        {
+                            "type": "drug_resistance",
+                            "drug": "rifampicin",
+                            "original_mutation": "p.Asp435Val",
+                            "confidence": "Assoc w R",
+                            "source": "WHO catalogue v2",
+                            "comment": ""
+                        },
+                        {
+                            "type": "drug_resistance",
+                            "drug": "rifampicin",
+                            "original_mutation": "RRDR non-silent",
+                            "confidence": "Assoc w R - Interim",
+                            "source": "WHO catalogue v2",
+                            "comment": "Expert rule: Non-silent variants in RRDR of rpoB"
+                        }
+                    ]
+                }
+            ],
+            "drugs": [
+                {
+                    "type": "drug_resistance",
+                    "drug": "rifampicin",
+                    "original_mutation": "p.Asp435Val",
+                    "confidence": "Assoc w R",
+                    "source": "WHO catalogue v2",
+                    "comment": ""
+                }
+            ],
+            "locus_tag": "Rv0667",
+            "gene_associated_drugs": [
+                "rifampicin"
+            ]
+        }
+    ],
+    "other_variants": [
+        {
+            "chrom": "Chromosome",
+            "pos": 763031,
+            "ref": "T",
+            "alt": "C",
+            "depth": 66,
+            "freq": 1.0,
+            "sv": false,
+            "filter": "pass",
+            "forward_reads": 29,
+            "reverse_reads": 37,
+            "sv_len": null,
+            "gene_id": "Rv0667",
+            "gene_name": "rpoB",
+            "feature_id": "CCP43410",
+            "type": "synonymous_variant",
+            "change": "c.3225T>C",
+            "nucleotide_change": "c.3225T>C",
+            "protein_change": "p.Ala1075Ala",
+            "annotation": [
+                {
+                    "type": "who_confidence",
+                    "drug": "rifampicin",
+                    "original_mutation": "c.3225T>C",
+                    "confidence": "Not assoc w R",
+                    "source": "WHO catalogue v2",
+                    "comment": ""
+                }
+            ],
+            "consequences": [
+                {
+                    "gene_id": "Rv0667",
+                    "gene_name": "rpoB",
+                    "feature_id": "CCP43410",
+                    "type": "synonymous_variant",
+                    "nucleotide_change": "c.3225T>C",
+                    "protein_change": "p.Ala1075Ala",
+                    "annotation": [
+                        {
+                            "type": "who_confidence",
+                            "drug": "rifampicin",
+                            "original_mutation": "c.3225T>C",
+                            "confidence": "Not assoc w R",
+                            "source": "WHO catalogue v2",
+                            "comment": ""
+                        }
+                    ]
+                },
+                {
+                    "gene_id": "Rv0668",
+                    "gene_name": "rpoC",
+                    "feature_id": "CCP43411",
+                    "type": "upstream_gene_variant",
+                    "nucleotide_change": "c.-339T>C",
+                    "protein_change": "",
+                    "annotation": []
+                }
+            ],
+            "locus_tag": "Rv0667",
+            "gene_associated_drugs": [
+                "rifampicin"
+            ]
+        },
+        {
+            "chrom": "Chromosome",
+            "pos": 1834177,
+            "ref": "A",
+            "alt": "C",
+            "depth": 67,
+            "freq": 1.0,
+            "sv": false,
+            "filter": "pass",
+            "forward_reads": 40,
+            "reverse_reads": 27,
+            "sv_len": null,
+            "gene_id": "Rv1630",
+            "gene_name": "rpsA",
+            "feature_id": "CCP44394",
+            "type": "synonymous_variant",
+            "change": "c.636A>C",
+            "nucleotide_change": "c.636A>C",
+            "protein_change": "p.Arg212Arg",
+            "annotation": [
+                {
+                    "type": "who_confidence",
+                    "drug": "pyrazinamide",
+                    "original_mutation": "c.636A>C",
+                    "confidence": "Not assoc w R - Interim",
+                    "source": "WHO catalogue v2",
+                    "comment": ""
+                }
+            ],
+            "consequences": [
+                {
+                    "gene_id": "Rv1630",
+                    "gene_name": "rpsA",
+                    "feature_id": "CCP44394",
+                    "type": "synonymous_variant",
+                    "nucleotide_change": "c.636A>C",
+                    "protein_change": "p.Arg212Arg",
+                    "annotation": [
+                        {
+                            "type": "who_confidence",
+                            "drug": "pyrazinamide",
+                            "original_mutation": "c.636A>C",
+                            "confidence": "Not assoc w R - Interim",
+                            "source": "WHO catalogue v2",
+                            "comment": ""
+                        }
+                    ]
+                }
+            ],
+            "locus_tag": "Rv1630",
+            "gene_associated_drugs": [
+                "pyrazinamide"
+            ]
+        }
+    ],
+    "qc_fail_variants": [],
+    "qc": {
+        "percent_reads_mapped": 87.19,
+        "num_reads_mapped": 5507,
+        "target_median_depth": 0.0,
+        "genome_median_depth": 0.0,
+        "target_qc": [
+            {
+                "target": "dnaA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "gyrB",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "gyrA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv0010c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fgd1",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mshA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ccsA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv0565c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "hadA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "nusG",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rpoB",
+                "percent_depth_pass": 100.0,
+                "median_depth": 75.0
+            },
+            {
+                "target": "rpoC",
+                "percent_depth_pass": 6.61,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mmpL5",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mmpS5",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mmpR5",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rpsL",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rplC",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv1129c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fbiC",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "sigE",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv1258c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "embR",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "atpE",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rrs",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rrl",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fabG1",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "inhA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rpsA",
+                "percent_depth_pass": 8.91,
+                "median_depth": 0.0
+            },
+            {
+                "target": "tsnR",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "tlyA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "bacA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ndh",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "katG",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "PPE35",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv1979c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "pncA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "kasA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "eis",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ahpC",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "folC",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv2477c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "pepQ",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ribD",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv2680",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv2681",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv2752c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "thyX",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "thyA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ald",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fbiD",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv3083",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "whiB7",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "Rv3236c",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "lpqB",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mtrB",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "mtrA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fbiA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "fbiB",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "alr",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "rpoA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ddn",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "clpC1",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "panD",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "glpK",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "embC",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "embA",
+                "percent_depth_pass": 3.98,
+                "median_depth": 0.0
+            },
+            {
+                "target": "embB",
+                "percent_depth_pass": 3.89,
+                "median_depth": 0.0
+            },
+            {
+                "target": "aftB",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ubiA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ethA",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "ethR",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "whiB6",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            },
+            {
+                "target": "gid",
+                "percent_depth_pass": 0.0,
+                "median_depth": 0.0
+            }
+        ],
+        "missing_positions": [
+        ]
+    },
+    "linked_samples": []
+}