Mercurial > repos > iuc > tbvcfreport

changeset 3:42818629ec4c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 4934c0ac6197
children 9793bc5d741b
files tbvcfreport.xml test-data/rif_resistant.results.json test-data/rif_resistant.vcf test-data/rif_resistant_drug_resistance_report.html test-data/rif_resistant_drug_resistance_report.txt test-data/rif_resistant_variants_report.html test-data/rif_resistant_variants_report.txt test-data/rif_resistant_variants_report_with_lineage.html test-data/rif_resistant_variants_report_with_lineage.txt test-data/vcf_with_no_protein_report.html test-data/vcf_with_no_protein_report.txt
diffstat 11 files changed, 2131 insertions(+), 256 deletions(-) [+]
line wrap: on
line diff
--- a/tbvcfreport.xml	Thu Mar 17 07:33:00 2022 +0000
+++ b/tbvcfreport.xml	Fri May 31 20:06:49 2024 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
-<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0">
+<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="AGPL-3.0-or-later">
   <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
   <macros>
-    <token name="@TOOL_VERSION@">0.1.10</token>
+    <token name="@TOOL_VERSION@">1.0.0</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
@@ -62,7 +62,7 @@
   <inputs>
     <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" />
     <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" />
-    <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
+    <param argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
     <section name="adv" title="Advanced options" expanded="false">
       <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify COMBAT-TB-NeoDB URI" help="For people with their own deployment of COMBAT-TB-NeoDB" />
     </section>
@@ -102,7 +102,7 @@
     <![CDATA[
     **tbvcfreport - @TOOL_VERSION@**
 
-    **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB (https://neodb.sanbi.ac.za) 
+    **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB  
     and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/).
 
     **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report.
--- 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": []
+}
--- a/test-data/rif_resistant.vcf	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant.vcf	Fri May 31 20:06:49 2024 +0000
@@ -1,53 +1,51 @@
 ##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
-##bcftoolsVersion=1.9+htslib-1.9
-##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam
-##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa
-##contig=<ID=MT_H37RV_BRD_V5,length=4411532>
-##ALT=<ID=*,Description="Represents allele(s) other than observed.">
-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
-##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
-##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
-##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
-##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
-##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
-##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
-##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
-##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##fileDate=20240531
+##source=freeBayes v1.3.2-dirty
+##reference=reference/ref.fa
+##contig=<ID=Chromosome,length=4411532>
+##phasing=none
+##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region Chromosome:0-1495040"
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
-##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
-##bcftools_callVersion=1.9+htslib-1.9
-##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr  2 06:47:33 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	rif_resistant.bam
-MT_H37RV_BRD_V5	15890	.	G	A	225.007	.	DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	154990	.	G	T	225.007	.	DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	346693	.	G	T	225.007	.	DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	449194	.	G	A	225.007	.	DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	497491	.	G	A	225.007	.	DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	761110	.	A	T	225.007	.	DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	763031	.	T	C	225.007	.	DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	811753	.	C	T	225.007	.	DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	1565566	.	C	T	225.007	.	DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	1833729	.	TCCCC	TCCCCCC	12.7055	.	INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999	GT:PL	1:50,3,0
-MT_H37RV_BRD_V5	1834177	.	A	C	225.007	.	DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	1849051	.	C	T	225.007	.	DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	2505085	.	G	A	225.007	.	DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	2543395	.	T	C	225.007	.	DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	2640807	.	G	A	225.007	.	DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	2775361	.	C	T	225.007	.	DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	2789798	.	G	T	225.007	.	DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	3477942	.	A	G	225.007	.	DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	3587446	.	G	A	225.007	.	DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	4254431	.	G	A	225.007	.	DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999	GT:PL	1:255,0
-MT_H37RV_BRD_V5	4254477	.	T	C	225.007	.	DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999	GT:PL	1:255,0
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##bcftools_viewVersion=1.13+htslib-1.13
+##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Fri May 31 19:43:23 2024
+##bcftools_annotateVersion=1.13+htslib-1.13
+##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Fri May 31 19:43:24 2024
+##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
+##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-utr ref snps.filt.vcf "
+##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
+##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	rif_resistant_fastq_gz
+Chromosome	15890	.	G	A	1500.92	.	AB=0;AO=48;DP=48;QA=1704;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0014c|GENE_Rv0014c|transcript|TRANSCRIPT_Rv0014c|protein_coding|1/1|c.1581C>T|p.Ser527Ser|1581/1881|1581/1881|527/626||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:48:1704:-153.63,-14.4494,0
+Chromosome	154990	.	G	T	1358.62	.	AB=0;AO=45;DP=45;QA=1558;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0127|GENE_Rv0127|transcript|TRANSCRIPT_Rv0127|protein_coding|1/1|c.759G>T|p.Arg253Arg|759/1368|759/1368|253/455||	GT:DP:RO:QR:AO:QA:GL	1/1:45:0:0:45:1558:-140.494,-13.5464,0
+Chromosome	346693	.	G	T	635.034	.	AB=0;AO=20;DP=20;QA=729;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0284|GENE_Rv0284|transcript|TRANSCRIPT_Rv0284|protein_coding|1/1|c.1059G>T|p.Ser353Ser|1059/3993|1059/3993|353/1330||	GT:DP:RO:QR:AO:QA:GL	1/1:20:0:0:20:729:-65.9317,-6.0206,0
+Chromosome	449194	.	G	A	651.409	.	AB=0;AO=23;DP=23;QA=782;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0372c|GENE_Rv0372c|transcript|TRANSCRIPT_Rv0372c|protein_coding|1/1|c.192C>T|p.Gly64Gly|192/756|192/756|64/251||	GT:DP:RO:QR:AO:QA:GL	1/1:23:0:0:23:782:-70.6929,-6.92369,0
+Chromosome	497491	.	G	A	1816.74	.	AB=0;AO=56;DP=56;QA=2057;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0411c|GENE_Rv0411c|transcript|TRANSCRIPT_Rv0411c|protein_coding|1/1|c.810C>T|p.Asp270Asp|810/987|810/987|270/328||	GT:DP:RO:QR:AO:QA:GL	1/1:56:0:0:56:2057:-185.366,-16.8577,0
+Chromosome	761110	.	A	T	1500.1	.	AB=0;AO=47;DP=48;QA=1701;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0667|GENE_Rv0667|transcript|TRANSCRIPT_Rv0667|protein_coding|1/1|c.1304A>T|p.Asp435Val|1304/3519|1304/3519|435/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:47:1701:-153.05,-14.1484,0
+Chromosome	811753	.	C	T	1585.34	.	AB=0;AO=48;DP=48;QA=1796;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0715|GENE_Rv0715|transcript|TRANSCRIPT_Rv0715|protein_coding|1/1|c.12C>T|p.His4His|12/318|12/318|4/105||	GT:DP:RO:QR:AO:QA:GL	1/1:48:0:0:48:1796:-161.892,-14.4494,0
+Chromosome	1565566	.	C	T	1332.75	.	AB=0;AO=43;DP=43;QA=1534;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1391|GENE_Rv1391|transcript|TRANSCRIPT_Rv1391|protein_coding|1/1|c.126C>T|p.Pro42Pro|126/1257|126/1257|42/418||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1534:-138.344,-12.9443,0
+Chromosome	1834177	.	A	C	1769.09	.	AB=0;AO=54;DP=54;QA=2006;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1630|GENE_Rv1630|transcript|TRANSCRIPT_Rv1630|protein_coding|1/1|c.636A>C|p.Arg212Arg|636/1446|636/1446|212/481||	GT:DP:RO:QR:AO:QA:GL	1/1:54:0:0:54:2006:-180.776,-16.2556,0
+Chromosome	1849051	.	C	T	2143.76	.	AB=0;AO=65;DP=65;QA=2415;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1640c|GENE_Rv1640c|transcript|TRANSCRIPT_Rv1640c|protein_coding|1/1|c.2985G>A|p.Pro995Pro|2985/3519|2985/3519|995/1172||	GT:DP:RO:QR:AO:QA:GL	1/1:65:0:0:65:2415:-217.563,-19.567,0
+Chromosome	2505085	.	G	A	1199.98	.	AB=0;AO=39;DP=39;QA=1425;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2231c|GENE_Rv2231c|transcript|TRANSCRIPT_Rv2231c|protein_coding|1/1|c.615C>T|p.Ala205Ala|615/1095|615/1095|205/364||	GT:DP:RO:QR:AO:QA:GL	1/1:39:0:0:39:1425:-128.53,-11.7402,0
+Chromosome	2543395	.	T	C	1871.23	.	AB=0;AO=58;DP=58;QA=2110;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2268c|GENE_Rv2268c|transcript|TRANSCRIPT_Rv2268c|protein_coding|1/1|c.882A>G|p.Glu294Glu|882/1470|882/1470|294/489||	GT:DP:RO:QR:AO:QA:GL	1/1:58:0:0:58:2110:-190.142,-17.4597,0
+Chromosome	2640807	.	G	A	1341.77	.	AB=0;AO=43;DP=43;QA=1519;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2357c|GENE_Rv2357c|transcript|TRANSCRIPT_Rv2357c|protein_coding|1/1|c.258C>T|p.Val86Val|258/1392|258/1392|86/463||	GT:DP:RO:QR:AO:QA:GL	1/1:43:0:0:43:1519:-136.983,-12.9443,0
+Chromosome	2775361	.	C	T	2221.3	.	AB=0;AO=69;DP=69;QA=2506;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2472|GENE_Rv2472|transcript|TRANSCRIPT_Rv2472|protein_coding|1/1|c.90C>T|p.Arg30Arg|90/294|90/294|30/97||	GT:DP:RO:QR:AO:QA:GL	1/1:69:0:0:69:2506:-225.745,-20.7711,0
+Chromosome	2789798	.	G	T	2050.68	.	AB=0;AO=62;DP=62;QA=2312;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2483c|GENE_Rv2483c|transcript|TRANSCRIPT_Rv2483c|protein_coding|1/1|c.1225C>A|p.Arg409Arg|1225/1743|1225/1743|409/580||	GT:DP:RO:QR:AO:QA:GL	1/1:62:0:0:62:2312:-208.29,-18.6639,0
+Chromosome	3477942	.	A	G	2414.91	.	AB=0;AO=75;DP=75;QA=2721;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3109|GENE_Rv3109|transcript|TRANSCRIPT_Rv3109|protein_coding|1/1|c.294A>G|p.Thr98Thr|294/1080|294/1080|98/359||	GT:DP:RO:QR:AO:QA:GL	1/1:75:0:0:75:2721:-245.092,-22.5773,0
+Chromosome	3587446	.	G	A	1562.41	.	AB=0;AO=49;DP=49;QA=1766;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3210c|GENE_Rv3210c|transcript|TRANSCRIPT_Rv3210c|protein_coding|1/1|c.94C>T|p.Leu32Leu|94/696|94/696|32/231||	GT:DP:RO:QR:AO:QA:GL	1/1:49:0:0:49:1766:-159.195,-14.7505,0
+Chromosome	4254431	.	G	A	1391.26	.	AB=0;AO=46;DP=46;QA=1617;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1518C>T|p.Asp506Asp|1518/1569|1518/1569|506/522||	GT:DP:RO:QR:AO:QA:GL	1/1:46:0:0:46:1617:-145.801,-13.8474,0
+Chromosome	4254477	.	T	C	760.909	.	AB=0;AO=26;DP=26;QA=933;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1472A>G|p.His491Arg|1472/1569|1472/1569|491/522||	GT:DP:RO:QR:AO:QA:GL	1/1:26:0:0:26:933:-84.2834,-7.82678,0
--- a/test-data/rif_resistant_drug_resistance_report.html	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_drug_resistance_report.html	Fri May 31 20:06:49 2024 +0000
@@ -21,120 +21,167 @@
                 rif_resistant Report
             </h2>
         </div>
+                <div class="row">
+            <table class="table table-striped table-hover table-responsive-md">
+                <caption>Lineage Info</caption>
+                <thead class="thead-light">
+                    <tr>
+                        <th scope="col">Lineage</th>
+                        <th scope="col">Lineage support fraction</th>
+                        <th scope="col">Family</th>
+                        <th scope="col">RD</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    <tr>
+                                                <td>lineage2</td>
+                                                <td>0.9940119760479041</td>
+                                                <td>East-Asian</td>
+                                                <td>RD105</td>
+                                            </tr>
+                                        <tr>
+                                                <td>lineage2.2.2</td>
+                                                <td>1.0</td>
+                                                <td>East-Asian (Beijing)</td>
+                                                <td>RD105;RD207</td>
+                                            </tr>
+                                    </tbody>
+            </table>
+        </div>
                         <hr>
         <div class="row">
     <h3 class="mb-2">
         <a class="text-body" href="https://github.com/jodyphelan/TBProfiler" target="_blank"
-            rel="noreferrer noopener">TBProfiler</a>
+            rel="noreferrer noopener">TB-Profiler</a>
         Drug Resistance Report
     </h3>
 </div>
 <div class="row">
-    <table id="drug_resistance" class="table table-hover table-bordered table-striped table-sm" cellspacing="0">
-        <caption class="mb-3 text-info">
-            <strong>Disclaimer</strong>:
-            Drug resistance predictions are for <strong>Research Purposes Only</strong> and are produced by
-            <a class="text-info" href="https://github.com/jodyphelan/TBProfiler" target="_blank"
-                rel="noreferrer noopener">TBProfiler</a>.
-        </caption>
-        <thead class="thead-light">
-            <tr>
-                <th scope="col">Drug</th>
-                <th scope="col">Resistance</th>
-                <th scope="col">Supporting Mutations</th>
-            </tr>
-        </thead>
-                <tr>
-            <td>Isoniazid</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Rifampicin</td>
-            <td>R</td>
-            <td>                <a target="_blank" href="https://explorer.sanbi.ac.za/gene?q=rpoB"
-                    rel="noreferrer noopener">rpoB</a>
-                (1.0 p.Asp435Val)
-                </td>
-        </tr>
-                <tr>
-            <td>Ethambutol</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Pyrazinamide</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Streptomycin</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Ethionamide</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Fluoroquinolones</td>
-            <td>S</td>
-            <td></td>
-        </tr>
+    <div class="col-md-12">
+        <p>TB-Profiler version 6.2.1 with
+            database tbdb:82777ea (Sun Mar 17 01:14:00 2024 +0000)</p>
+</div>
+<div class="row">
+    <div class="col-md-12">
+        <table id="drug_resistance" class="table table-hover table-bordered table-striped table-responsive-md" cellspacing="0">
+            <caption class="mb-3 text-info">
+                <strong>Disclaimer</strong>:
+                Drug resistance predictions are for <strong>Research Purposes Only</strong> and are produced by
+                <a class="text-info" href="https://github.com/jodyphelan/TBProfiler" target="_blank"
+                    rel="noreferrer noopener">TB-Profiler</a>.
+            </caption>
+            <thead class="thead-light">
                 <tr>
-            <td>Amikacin</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Capreomycin</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Kanamycin</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Para-aminosalicylic acid</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Linezolid</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Cycloserine</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Delaminid</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Clofazimine</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-                <tr>
-            <td>Bedaquiline</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-        </tr>
-                <tr>
-            <td>Aminoglycosides</td>
-            <td>S</td>
-            <td></td>
-        </tr>
-
-            </table>
+                    <th scope="col">Drug</th>
+                    <th scope="col">Resistance</th>
+                    <th scope="col">Supporting Mutations</th>
+                </tr>
+            </thead>
+                        <tr>
+                <td>Isoniazid</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Rifampicin</td>
+                <td>R</td>
+                <td>                    <a target="_blank" href="https://explorer.sanbi.ac.za/gene?q=rpoB"
+                        rel="noreferrer noopener">rpoB</a>
+                    (1.0 p.Asp435Val)
+                    </td>
+            </tr>
+                        <tr>
+                <td>Ethambutol</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Pyrazinamide</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Streptomycin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Ethionamide</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Fluoroquinolones</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Amikacin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Capreomycin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Kanamycin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Para-aminosalicylic acid</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Linezolid</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Cycloserine</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Delamanid</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Clofazimine</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Bedaquiline</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Aminoglycosides</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Levofloxacin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Moxifloxacin</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                        <tr>
+                <td>Pretomanid</td>
+                <td>S</td>
+                <td></td>
+            </tr>
+                    </table>
+    </div>
 </div>
                 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
             integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">
--- a/test-data/rif_resistant_drug_resistance_report.txt	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_drug_resistance_report.txt	Fri May 31 20:06:49 2024 +0000
@@ -1,10 +1,9 @@
 #Rif_resistant Report
-#Lineage	Family	Spoligotype	RD	Agreement
-lineage2	East-Asian	Beijing	RD105	1.0
-lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	1.0
-lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207	1.0
+#Lineage	Support	Family	RD
+lineage2	0.9940119760479041	East-Asian	RD105
+lineage2.2.2	1.0	East-Asian (Beijing)	RD105;RD207
 
-#TBProfiler Drug Resistance Report
+#TB-Profiler Drug Resistance Report
 
 #Drug	Resistance	Supporting Mutations
 Isoniazid	S	
@@ -20,9 +19,12 @@
 Para-aminosalicylic acid	S	
 Linezolid	S	
 Cycloserine	S	
-Delaminid	S	
+Delamanid	S	
 Clofazimine	S	
 Bedaquiline	S	
 Aminoglycosides	S	
+Levofloxacin	S	
+Moxifloxacin	S	
+Pretomanid	S	
 
-#Drug resistance predictions are for research purposes only and are produced by the TBProfiler software.
+#Drug resistance predictions are for research purposes only and are produced by the TB-Profiler software.
--- a/test-data/rif_resistant_variants_report.html	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_variants_report.html	Fri May 31 20:06:49 2024 +0000
@@ -22,10 +22,545 @@
             </h2>
         </div>
                         <hr>
-        <div>
-    <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html"
-            target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p>
-    <p>Kindly check if the '<strong>ANN</strong>' field is present.</p>
+        <div class="row justify-content-center align-items-center">
+    <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
+        <thead class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">IS_SNV</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </thead>
+        <tbody>
+
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0014c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0014c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"
+                        target="_blank" rel="noreferrer noopener">15890</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1581C>T</td>
+                <td>p.Ser527Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0127</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0127</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"
+                        target="_blank" rel="noreferrer noopener">154990</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.759G>T</td>
+                <td>p.Arg253Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0284</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0284</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None"
+                        target="_blank" rel="noreferrer noopener">346693</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1059G>T</td>
+                <td>p.Ser353Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0372c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0372c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None"
+                        target="_blank" rel="noreferrer noopener">449194</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.192C>T</td>
+                <td>p.Gly64Gly</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0411c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0411c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None"
+                        target="_blank" rel="noreferrer noopener">497491</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.810C>T</td>
+                <td>p.Asp270Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0667</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0667</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None"
+                        target="_blank" rel="noreferrer noopener">761110</a>
+                </td>
+                <td>A</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1304A>T</td>
+                <td>p.Asp435Val</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0715</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0715</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None"
+                        target="_blank" rel="noreferrer noopener">811753</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.12C>T</td>
+                <td>p.His4His</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1391</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1391</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None"
+                        target="_blank" rel="noreferrer noopener">1565566</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.126C>T</td>
+                <td>p.Pro42Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1630</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1630</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None"
+                        target="_blank" rel="noreferrer noopener">1834177</a>
+                </td>
+                <td>A</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.636A>C</td>
+                <td>p.Arg212Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1640c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1640c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None"
+                        target="_blank" rel="noreferrer noopener">1849051</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.2985G>A</td>
+                <td>p.Pro995Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2231c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2231c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None"
+                        target="_blank" rel="noreferrer noopener">2505085</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.615C>T</td>
+                <td>p.Ala205Ala</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2268c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2268c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None"
+                        target="_blank" rel="noreferrer noopener">2543395</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.882A>G</td>
+                <td>p.Glu294Glu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2357c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2357c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None"
+                        target="_blank" rel="noreferrer noopener">2640807</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.258C>T</td>
+                <td>p.Val86Val</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2472</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2472</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None"
+                        target="_blank" rel="noreferrer noopener">2775361</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.90C>T</td>
+                <td>p.Arg30Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2483c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2483c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None"
+                        target="_blank" rel="noreferrer noopener">2789798</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1225C>A</td>
+                <td>p.Arg409Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3109</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3109</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None"
+                        target="_blank" rel="noreferrer noopener">3477942</a>
+                </td>
+                <td>A</td>
+                <td>G</td>
+                <td>protein_coding</td>
+                <td>c.294A>G</td>
+                <td>p.Thr98Thr</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3210c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3210c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"
+                        target="_blank" rel="noreferrer noopener">3587446</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.94C>T</td>
+                <td>p.Leu32Leu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"
+                        target="_blank" rel="noreferrer noopener">4254431</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1518C>T</td>
+                <td>p.Asp506Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"
+                        target="_blank" rel="noreferrer noopener">4254477</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.1472A>G</td>
+                <td>p.His491Arg</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                    </tbody>
+        <tfoot class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">TYPE</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </tfoot>
+    </table>
+</div>
+</main>
+<div class="mt-5">
 </div>
                 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
             integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">
--- a/test-data/rif_resistant_variants_report.txt	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_variants_report.txt	Fri May 31 20:06:49 2024 +0000
@@ -1,4 +1,22 @@
 #Rif_resistant Report
-#Lineage	Family	Spoligotype	RD	Agreement
 
-#CHR	GENE	IDENTIFIER	PRODUCT	TYPE	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHAWAY
+#CHR	GENE	IDENTIFIER	PRODUCT	IS_SNV	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
+Chromosome	Rv0014c	GENE_Rv0014c	NOPROTEIN	True	synonymous_variant	15890	G	A	p.Ser527Ser	LOW	
+Chromosome	Rv0127	GENE_Rv0127	NOPROTEIN	True	synonymous_variant	154990	G	T	p.Arg253Arg	LOW	
+Chromosome	Rv0284	GENE_Rv0284	NOPROTEIN	True	synonymous_variant	346693	G	T	p.Ser353Ser	LOW	
+Chromosome	Rv0372c	GENE_Rv0372c	NOPROTEIN	True	synonymous_variant	449194	G	A	p.Gly64Gly	LOW	
+Chromosome	Rv0411c	GENE_Rv0411c	NOPROTEIN	True	synonymous_variant	497491	G	A	p.Asp270Asp	LOW	
+Chromosome	Rv0667	GENE_Rv0667	NOPROTEIN	True	missense_variant	761110	A	T	p.Asp435Val	MODERATE	
+Chromosome	Rv0715	GENE_Rv0715	NOPROTEIN	True	synonymous_variant	811753	C	T	p.His4His	LOW	
+Chromosome	Rv1391	GENE_Rv1391	NOPROTEIN	True	synonymous_variant	1565566	C	T	p.Pro42Pro	LOW	
+Chromosome	Rv1630	GENE_Rv1630	NOPROTEIN	True	synonymous_variant	1834177	A	C	p.Arg212Arg	LOW	
+Chromosome	Rv1640c	GENE_Rv1640c	NOPROTEIN	True	synonymous_variant	1849051	C	T	p.Pro995Pro	LOW	
+Chromosome	Rv2231c	GENE_Rv2231c	NOPROTEIN	True	synonymous_variant	2505085	G	A	p.Ala205Ala	LOW	
+Chromosome	Rv2268c	GENE_Rv2268c	NOPROTEIN	True	synonymous_variant	2543395	T	C	p.Glu294Glu	LOW	
+Chromosome	Rv2357c	GENE_Rv2357c	NOPROTEIN	True	synonymous_variant	2640807	G	A	p.Val86Val	LOW	
+Chromosome	Rv2472	GENE_Rv2472	NOPROTEIN	True	synonymous_variant	2775361	C	T	p.Arg30Arg	LOW	
+Chromosome	Rv2483c	GENE_Rv2483c	NOPROTEIN	True	synonymous_variant	2789798	G	T	p.Arg409Arg	LOW	
+Chromosome	Rv3109	GENE_Rv3109	NOPROTEIN	True	synonymous_variant	3477942	A	G	p.Thr98Thr	LOW	
+Chromosome	Rv3210c	GENE_Rv3210c	NOPROTEIN	True	synonymous_variant	3587446	G	A	p.Leu32Leu	LOW	
+Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	synonymous_variant	4254431	G	A	p.Asp506Asp	LOW	
+Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	missense_variant	4254477	T	C	p.His491Arg	MODERATE	
--- a/test-data/rif_resistant_variants_report_with_lineage.html	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_variants_report_with_lineage.html	Fri May 31 20:06:49 2024 +0000
@@ -21,6 +21,33 @@
                 rif_resistant Report
             </h2>
         </div>
+                <div class="row">
+            <table class="table table-striped table-hover table-responsive-md">
+                <caption>Lineage Info</caption>
+                <thead class="thead-light">
+                    <tr>
+                        <th scope="col">Lineage</th>
+                        <th scope="col">Lineage support fraction</th>
+                        <th scope="col">Family</th>
+                        <th scope="col">RD</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    <tr>
+                                                <td>lineage2</td>
+                                                <td>0.9940119760479041</td>
+                                                <td>East-Asian</td>
+                                                <td>RD105</td>
+                                            </tr>
+                                        <tr>
+                                                <td>lineage2.2.2</td>
+                                                <td>1.0</td>
+                                                <td>East-Asian (Beijing)</td>
+                                                <td>RD105;RD207</td>
+                                            </tr>
+                                    </tbody>
+            </table>
+        </div>
                         <hr>
         <div class="row justify-content-center align-items-center">
     <table id="lineagereport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
@@ -35,33 +62,561 @@
         </thead>
         <tbody>
                         <tr>
-                <td>lineage2</td>
-                <td>East-Asian</td>
-                <td>Beijing</td>
-                <td>RD105</td>
-                <td>1.0</td>
+                <td></td>
+                <td></td>
+                <td></td>
+                <td></td>
+                <td></td>
             </tr>
                         <tr>
-                <td>lineage2.2</td>
-                <td>East-Asian (Beijing)</td>
-                <td>Beijing-RD207</td>
-                <td>RD105;RD207</td>
-                <td>1.0</td>
-            </tr>
-                        <tr>
-                <td>lineage2.2.2</td>
-                <td>East-Asian (Beijing)</td>
-                <td>Beijing-RD105/RD207</td>
-                <td>RD105;RD207</td>
-                <td>1.0</td>
+                <td></td>
+                <td></td>
+                <td></td>
+                <td></td>
+                <td></td>
             </tr>
                     </tbody>
     </table>
 </div>
-<div>
-    <p>No variant data was found for this VCF file. Is it a <a href="http://snpeff.sourceforge.net/SnpEff_manual.html"
-            target="_blank" rel="noreferrer noopener">SnpEff</a> annotated VCF file?</p>
-    <p>Kindly check if the '<strong>ANN</strong>' field is present.</p>
+<div class="row justify-content-center align-items-center">
+    <table id="vcfreport" class="table table-bordered table-striped table-hover table-sm" cellspacing="0">
+        <thead class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">IS_SNV</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </thead>
+        <tbody>
+
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0014c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0014c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0014c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A15890..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A15890..None"
+                        target="_blank" rel="noreferrer noopener">15890</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1581C>T</td>
+                <td>p.Ser527Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0127</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0127" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0127</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A154990..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A154990..None"
+                        target="_blank" rel="noreferrer noopener">154990</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.759G>T</td>
+                <td>p.Arg253Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0284</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0284" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0284</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A346693..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A346693..None"
+                        target="_blank" rel="noreferrer noopener">346693</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1059G>T</td>
+                <td>p.Ser353Ser</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0372c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0372c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0372c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A449194..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A449194..None"
+                        target="_blank" rel="noreferrer noopener">449194</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.192C>T</td>
+                <td>p.Gly64Gly</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0411c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0411c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0411c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A497491..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A497491..None"
+                        target="_blank" rel="noreferrer noopener">497491</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.810C>T</td>
+                <td>p.Asp270Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0667</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0667" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0667</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A761110..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A761110..None"
+                        target="_blank" rel="noreferrer noopener">761110</a>
+                </td>
+                <td>A</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1304A>T</td>
+                <td>p.Asp435Val</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv0715</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv0715" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv0715</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A811753..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A811753..None"
+                        target="_blank" rel="noreferrer noopener">811753</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.12C>T</td>
+                <td>p.His4His</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1391</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1391" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1391</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1565566..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1565566..None"
+                        target="_blank" rel="noreferrer noopener">1565566</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.126C>T</td>
+                <td>p.Pro42Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1630</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1630" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1630</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1834177..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1834177..None"
+                        target="_blank" rel="noreferrer noopener">1834177</a>
+                </td>
+                <td>A</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.636A>C</td>
+                <td>p.Arg212Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv1640c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv1640c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv1640c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A1849051..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A1849051..None"
+                        target="_blank" rel="noreferrer noopener">1849051</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.2985G>A</td>
+                <td>p.Pro995Pro</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2231c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2231c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2231c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2505085..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2505085..None"
+                        target="_blank" rel="noreferrer noopener">2505085</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.615C>T</td>
+                <td>p.Ala205Ala</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2268c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2268c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2268c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2543395..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2543395..None"
+                        target="_blank" rel="noreferrer noopener">2543395</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.882A>G</td>
+                <td>p.Glu294Glu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2357c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2357c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2357c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2640807..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2640807..None"
+                        target="_blank" rel="noreferrer noopener">2640807</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.258C>T</td>
+                <td>p.Val86Val</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2472</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2472" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2472</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2775361..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2775361..None"
+                        target="_blank" rel="noreferrer noopener">2775361</a>
+                </td>
+                <td>C</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.90C>T</td>
+                <td>p.Arg30Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv2483c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv2483c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv2483c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A2789798..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A2789798..None"
+                        target="_blank" rel="noreferrer noopener">2789798</a>
+                </td>
+                <td>G</td>
+                <td>T</td>
+                <td>protein_coding</td>
+                <td>c.1225C>A</td>
+                <td>p.Arg409Arg</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3109</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3109" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3109</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3477942..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3477942..None"
+                        target="_blank" rel="noreferrer noopener">3477942</a>
+                </td>
+                <td>A</td>
+                <td>G</td>
+                <td>protein_coding</td>
+                <td>c.294A>G</td>
+                <td>p.Thr98Thr</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3210c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3210c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3210c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A3587446..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A3587446..None"
+                        target="_blank" rel="noreferrer noopener">3587446</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.94C>T</td>
+                <td>p.Leu32Leu</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>synonymous_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254431..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254431..None"
+                        target="_blank" rel="noreferrer noopener">4254431</a>
+                </td>
+                <td>G</td>
+                <td>A</td>
+                <td>protein_coding</td>
+                <td>c.1518C>T</td>
+                <td>p.Asp506Asp</td>
+                <td>LOW</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                        <tr>
+                <td>Chromosome</td>
+                <td>Rv3799c</td>
+                <td>
+                                        <a href="https://explorer.sanbi.ac.za/gene?q=GENE_Rv3799c" target="_blank"
+                        rel="noreferrer noopener">GENE_Rv3799c</a>
+                                    </td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+                <td>True</td>
+                <td>missense_variant</td>
+                <td>
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254477..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254477..None"
+                        target="_blank" rel="noreferrer noopener">4254477</a>
+                </td>
+                <td>T</td>
+                <td>C</td>
+                <td>protein_coding</td>
+                <td>c.1472A>G</td>
+                <td>p.His491Arg</td>
+                <td>MODERATE</td>
+                <td>
+                                        <p>NA</p>
+                                    </td>
+            </tr>
+                    </tbody>
+        <tfoot class="thead-light">
+            <tr>
+                <th scope="col">CHR</th>
+                <th scope="col">GENE</th>
+                <th scope="col">LOCUS</th>
+                <th scope="col">PRODUCT</th>
+                <th scope="col">TYPE</th>
+                <th scope="col">EFFECT</th>
+                <th scope="col">POS</th>
+                <th scope="col">REF</th>
+                <th scope="col">ALT</th>
+                <th scope="col">BIOTYPE</th>
+                <th scope="col">NUCLEOTIDE</th>
+                <th scope="col">CONSEQUENCE</th>
+                <th scope="col">IMPACT</th>
+                <th scope="col">PATHWAY</th>
+            </tr>
+        </tfoot>
+    </table>
+</div>
+</main>
+<div class="mt-5">
 </div>
                 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
             integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous">
--- a/test-data/rif_resistant_variants_report_with_lineage.txt	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/rif_resistant_variants_report_with_lineage.txt	Fri May 31 20:06:49 2024 +0000
@@ -1,7 +1,25 @@
 #Rif_resistant Report
-#Lineage	Family	Spoligotype	RD	Agreement
-lineage2	East-Asian	Beijing	RD105	1.0
-lineage2.2	East-Asian (Beijing)	Beijing-RD207	RD105;RD207	1.0
-lineage2.2.2	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207	1.0
+#Lineage	Support	Family	RD
+lineage2	0.9940119760479041	East-Asian	RD105
+lineage2.2.2	1.0	East-Asian (Beijing)	RD105;RD207
 
-#CHR	GENE	IDENTIFIER	PRODUCT	TYPE	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHAWAY
+#CHR	GENE	IDENTIFIER	PRODUCT	IS_SNV	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
+Chromosome	Rv0014c	GENE_Rv0014c	NOPROTEIN	True	synonymous_variant	15890	G	A	p.Ser527Ser	LOW	
+Chromosome	Rv0127	GENE_Rv0127	NOPROTEIN	True	synonymous_variant	154990	G	T	p.Arg253Arg	LOW	
+Chromosome	Rv0284	GENE_Rv0284	NOPROTEIN	True	synonymous_variant	346693	G	T	p.Ser353Ser	LOW	
+Chromosome	Rv0372c	GENE_Rv0372c	NOPROTEIN	True	synonymous_variant	449194	G	A	p.Gly64Gly	LOW	
+Chromosome	Rv0411c	GENE_Rv0411c	NOPROTEIN	True	synonymous_variant	497491	G	A	p.Asp270Asp	LOW	
+Chromosome	Rv0667	GENE_Rv0667	NOPROTEIN	True	missense_variant	761110	A	T	p.Asp435Val	MODERATE	
+Chromosome	Rv0715	GENE_Rv0715	NOPROTEIN	True	synonymous_variant	811753	C	T	p.His4His	LOW	
+Chromosome	Rv1391	GENE_Rv1391	NOPROTEIN	True	synonymous_variant	1565566	C	T	p.Pro42Pro	LOW	
+Chromosome	Rv1630	GENE_Rv1630	NOPROTEIN	True	synonymous_variant	1834177	A	C	p.Arg212Arg	LOW	
+Chromosome	Rv1640c	GENE_Rv1640c	NOPROTEIN	True	synonymous_variant	1849051	C	T	p.Pro995Pro	LOW	
+Chromosome	Rv2231c	GENE_Rv2231c	NOPROTEIN	True	synonymous_variant	2505085	G	A	p.Ala205Ala	LOW	
+Chromosome	Rv2268c	GENE_Rv2268c	NOPROTEIN	True	synonymous_variant	2543395	T	C	p.Glu294Glu	LOW	
+Chromosome	Rv2357c	GENE_Rv2357c	NOPROTEIN	True	synonymous_variant	2640807	G	A	p.Val86Val	LOW	
+Chromosome	Rv2472	GENE_Rv2472	NOPROTEIN	True	synonymous_variant	2775361	C	T	p.Arg30Arg	LOW	
+Chromosome	Rv2483c	GENE_Rv2483c	NOPROTEIN	True	synonymous_variant	2789798	G	T	p.Arg409Arg	LOW	
+Chromosome	Rv3109	GENE_Rv3109	NOPROTEIN	True	synonymous_variant	3477942	A	G	p.Thr98Thr	LOW	
+Chromosome	Rv3210c	GENE_Rv3210c	NOPROTEIN	True	synonymous_variant	3587446	G	A	p.Leu32Leu	LOW	
+Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	synonymous_variant	4254431	G	A	p.Asp506Asp	LOW	
+Chromosome	Rv3799c	GENE_Rv3799c	NOPROTEIN	True	missense_variant	4254477	T	C	p.His491Arg	MODERATE	
--- a/test-data/vcf_with_no_protein_report.html	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/vcf_with_no_protein_report.html	Fri May 31 20:06:49 2024 +0000
@@ -30,7 +30,7 @@
                 <th scope="col">GENE</th>
                 <th scope="col">LOCUS</th>
                 <th scope="col">PRODUCT</th>
-                <th scope="col">TYPE</th>
+                <th scope="col">IS_SNV</th>
                 <th scope="col">EFFECT</th>
                 <th scope="col">POS</th>
                 <th scope="col">REF</th>
@@ -55,10 +55,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O69720"
                         target="_blank" rel="noreferrer noopener">O69720</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..4200220&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..4200220"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4200220..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4200220..None"
                         target="_blank" rel="noreferrer noopener">4200220</a>
                 </td>
                 <td>G</td>
@@ -82,10 +82,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O69722"
                         target="_blank" rel="noreferrer noopener">O69722</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>synonymous_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..4202383&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..4202383"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4202383..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4202383..None"
                         target="_blank" rel="noreferrer noopener">4202383</a>
                 </td>
                 <td>C</td>
@@ -114,10 +114,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O69725"
                         target="_blank" rel="noreferrer noopener">O69725</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..4205120&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..4205120"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4205120..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4205120..None"
                         target="_blank" rel="noreferrer noopener">4205120</a>
                 </td>
                 <td>G</td>
@@ -146,10 +146,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O69729"
                         target="_blank" rel="noreferrer noopener">O69729</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..4210876&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..4210876"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4210876..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4210876..None"
                         target="_blank" rel="noreferrer noopener">4210876</a>
                 </td>
                 <td>C</td>
@@ -173,10 +173,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P72036"
                         target="_blank" rel="noreferrer noopener">P72036</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..4214747&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..4214747"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4214747..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4214747..None"
                         target="_blank" rel="noreferrer noopener">4214747</a>
                 </td>
                 <td>C</td>
@@ -200,10 +200,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P72037"
                         target="_blank" rel="noreferrer noopener">P72037</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..4215484&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..4215484"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4215484..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4215484..None"
                         target="_blank" rel="noreferrer noopener">4215484</a>
                 </td>
                 <td>C</td>
@@ -227,10 +227,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WML5"
                         target="_blank" rel="noreferrer noopener">P9WML5</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..4217557&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..4217557"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4217557..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4217557..None"
                         target="_blank" rel="noreferrer noopener">4217557</a>
                 </td>
                 <td>G</td>
@@ -277,10 +277,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P72043"
                         target="_blank" rel="noreferrer noopener">P72043</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..4223172&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..4223172"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4223172..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4223172..None"
                         target="_blank" rel="noreferrer noopener">4223172</a>
                 </td>
                 <td>C</td>
@@ -304,10 +304,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WKX1"
                         target="_blank" rel="noreferrer noopener">P9WKX1</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>synonymous_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..4232327&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..4232327"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4232327..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4232327..None"
                         target="_blank" rel="noreferrer noopener">4232327</a>
                 </td>
                 <td>G</td>
@@ -331,10 +331,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WN03"
                         target="_blank" rel="noreferrer noopener">P9WN03</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>synonymous_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..4238963&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..4238963"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4238963..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4238963..None"
                         target="_blank" rel="noreferrer noopener">4238963</a>
                 </td>
                 <td>C</td>
@@ -363,10 +363,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WN03"
                         target="_blank" rel="noreferrer noopener">P9WN03</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..4239274&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..4239274"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4239274..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4239274..None"
                         target="_blank" rel="noreferrer noopener">4239274</a>
                 </td>
                 <td>C</td>
@@ -395,10 +395,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WNL5"
                         target="_blank" rel="noreferrer noopener">P9WNL5</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..4240671&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..4240671"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4240671..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4240671..None"
                         target="_blank" rel="noreferrer noopener">4240671</a>
                 </td>
                 <td>T</td>
@@ -427,10 +427,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7"
                         target="_blank" rel="noreferrer noopener">P9WNL7</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..4247429&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..4247429"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247429..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247429..None"
                         target="_blank" rel="noreferrer noopener">4247429</a>
                 </td>
                 <td>A</td>
@@ -459,10 +459,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=P9WNL7"
                         target="_blank" rel="noreferrer noopener">P9WNL7</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..4247646&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..4247646"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4247646..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4247646..None"
                         target="_blank" rel="noreferrer noopener">4247646</a>
                 </td>
                 <td>C</td>
@@ -491,10 +491,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O53577"
                         target="_blank" rel="noreferrer noopener">O53577</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>synonymous_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..4251297&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..4251297"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4251297..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4251297..None"
                         target="_blank" rel="noreferrer noopener">4251297</a>
                 </td>
                 <td>C</td>
@@ -517,10 +517,10 @@
                 <td>
                                         <p>NA</p>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..4254290&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..4254290"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254290..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254290..None"
                         target="_blank" rel="noreferrer noopener">4254290</a>
                 </td>
                 <td>T</td>
@@ -544,10 +544,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O53578"
                         target="_blank" rel="noreferrer noopener">O53578</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..4254478&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..4254478"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4254478..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4254478..None"
                         target="_blank" rel="noreferrer noopener">4254478</a>
                 </td>
                 <td>G</td>
@@ -571,10 +571,10 @@
                                         <a href="https://explorer.sanbi.ac.za/search?q=O53580"
                         target="_blank" rel="noreferrer noopener">O53580</a>
                                     </td>
-                <td>snp</td>
+                <td>True</td>
                 <td>missense_variant</td>
                 <td>
-                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..4261499&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..4261499"
+                    <a href="https://explorer.sanbi.ac.za/jbrowse/?loc=NC_000962.3%3A4261499..None&tracks=DNA%2CGenes&highlight=NC_000962.3%3A4261499..None"
                         target="_blank" rel="noreferrer noopener">4261499</a>
                 </td>
                 <td>A</td>
--- a/test-data/vcf_with_no_protein_report.txt	Thu Mar 17 07:33:00 2022 +0000
+++ b/test-data/vcf_with_no_protein_report.txt	Fri May 31 20:06:49 2024 +0000
@@ -1,22 +1,21 @@
 #Vcf_with_no_protein Report
-#Lineage	Family	Spoligotype	RD	Agreement
 
-#CHR	GENE	IDENTIFIER	PRODUCT	TYPE	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
-Chromosome	Rv3753c	Rv3753c	O69720	snp	missense_variant	4200220	G	A	p.Thr1Met	MODERATE	
-Chromosome	Rv3756c	Rv3756c	O69722	snp	synonymous_variant	4202383	C	A	p.Val77Val	LOW	ABC transporters
-Chromosome	Rv3759c	Rv3759c	O69725	snp	missense_variant	4205120	G	A	p.Pro85Leu	MODERATE	ABC transporters
-Chromosome	Rv3764c	Rv3764c	O69729	snp	missense_variant	4210876	C	T	p.Arg45His	MODERATE	
-Chromosome	Rv3769	Rv3769	P72036	snp	missense_variant	4214747	C	T	p.His45Tyr	MODERATE	
-Chromosome	Rv3770c	Rv3770c	P72037	snp	missense_variant	4215484	C	G	p.Ala98Pro	MODERATE	
-Chromosome	Rv3772	Rv3772	P9WML5	snp	missense_variant	4217557	G	A	p.Ala142Thr	MODERATE	Phenylalanine, tyrosine and tryptophan biosynthesis,Phenylalanine metabolism,Histidine metabolism,Tyrosine metabolism
-Chromosome	Rv3777	Rv3777	P72043	snp	missense_variant	4223172	C	T	p.Ala160Val	MODERATE	
-Chromosome	Rv3785	Rv3785	P9WKX1	snp	synonymous_variant	4232327	G	A	p.Arg336Arg	LOW	
-Chromosome	Rv3792	Rv3792	P9WN03	snp	synonymous_variant	4238963	C	T	p.His344His	LOW	Arabinogalactan biosynthesis - Mycobacterium
-Chromosome	Rv3792	Rv3792	P9WN03	snp	missense_variant	4239274	C	G	p.Pro448Arg	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
-Chromosome	Rv3793	Rv3793	P9WNL5	snp	missense_variant	4240671	T	C	p.Ile270Thr	MODERATE	Lipoarabinomannan (LAM) biosynthesis
-Chromosome	Rv3795	Rv3795	P9WNL7	snp	missense_variant	4247429	A	G	p.Met306Val	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
-Chromosome	Rv3795	Rv3795	P9WNL7	snp	missense_variant	4247646	C	A	p.Ala378Glu	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
-Chromosome	Rv3797	Rv3797	O53577	snp	synonymous_variant	4251297	C	G	p.Gly71Gly	LOW	
-Chromosome	Rv3798	Rv3798	NOPROTEIN	snp	missense_variant	4254290	T	G	p.Leu433Arg	MODERATE	
-Chromosome	Rv3799c	Rv3799c	O53578	snp	missense_variant	4254478	G	A	p.His491Tyr	MODERATE	
-Chromosome	Rv3801c	Rv3801c	O53580	snp	missense_variant	4261499	A	G	p.Val523Ala	MODERATE	
+#CHR	GENE	IDENTIFIER	PRODUCT	IS_SNV	ANNOTATION	POS	REF	ALT	CONSEQUENCE	IMPACT	PATHWAY
+Chromosome	Rv3753c	Rv3753c	O69720	True	missense_variant	4200220	G	A	p.Thr1Met	MODERATE	
+Chromosome	Rv3756c	Rv3756c	O69722	True	synonymous_variant	4202383	C	A	p.Val77Val	LOW	ABC transporters
+Chromosome	Rv3759c	Rv3759c	O69725	True	missense_variant	4205120	G	A	p.Pro85Leu	MODERATE	ABC transporters
+Chromosome	Rv3764c	Rv3764c	O69729	True	missense_variant	4210876	C	T	p.Arg45His	MODERATE	
+Chromosome	Rv3769	Rv3769	P72036	True	missense_variant	4214747	C	T	p.His45Tyr	MODERATE	
+Chromosome	Rv3770c	Rv3770c	P72037	True	missense_variant	4215484	C	G	p.Ala98Pro	MODERATE	
+Chromosome	Rv3772	Rv3772	P9WML5	True	missense_variant	4217557	G	A	p.Ala142Thr	MODERATE	Phenylalanine, tyrosine and tryptophan biosynthesis,Phenylalanine metabolism,Histidine metabolism,Tyrosine metabolism
+Chromosome	Rv3777	Rv3777	P72043	True	missense_variant	4223172	C	T	p.Ala160Val	MODERATE	
+Chromosome	Rv3785	Rv3785	P9WKX1	True	synonymous_variant	4232327	G	A	p.Arg336Arg	LOW	
+Chromosome	Rv3792	Rv3792	P9WN03	True	synonymous_variant	4238963	C	T	p.His344His	LOW	Arabinogalactan biosynthesis - Mycobacterium
+Chromosome	Rv3792	Rv3792	P9WN03	True	missense_variant	4239274	C	G	p.Pro448Arg	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
+Chromosome	Rv3793	Rv3793	P9WNL5	True	missense_variant	4240671	T	C	p.Ile270Thr	MODERATE	Lipoarabinomannan (LAM) biosynthesis
+Chromosome	Rv3795	Rv3795	P9WNL7	True	missense_variant	4247429	A	G	p.Met306Val	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
+Chromosome	Rv3795	Rv3795	P9WNL7	True	missense_variant	4247646	C	A	p.Ala378Glu	MODERATE	Arabinogalactan biosynthesis - Mycobacterium
+Chromosome	Rv3797	Rv3797	O53577	True	synonymous_variant	4251297	C	G	p.Gly71Gly	LOW	
+Chromosome	Rv3798	Rv3798	NOPROTEIN	True	missense_variant	4254290	T	G	p.Leu433Arg	MODERATE	
+Chromosome	Rv3799c	Rv3799c	O53578	True	missense_variant	4254478	G	A	p.His491Tyr	MODERATE	
+Chromosome	Rv3801c	Rv3801c	O53580	True	missense_variant	4261499	A	G	p.Val523Ala	MODERATE