Created
July 14, 2023 17:05
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TBProfiler output when run on myco_sra for BioSample SAMEA11744634. TBProfiler was run on the fastqs this time, not the bams.
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| TBProfiler report | |
| ================= | |
| The following report has been generated by TBProfiler. | |
| Summary | |
| ------- | |
| ID: SAMEA11744634 | |
| Date: Mon Jul 10 17:53:25 2023 | |
| Strain: lineage4.2.2.2 | |
| Drug-resistance: MDR-TB | |
| Median Depth: 56 | |
| Lineage report | |
| -------------- | |
| Lineage Estimated Fraction Spoligotype Rd | |
| lineage4 1.000 LAM;T;S;X;H None | |
| lineage4.2 1.000 H;T;LAM None | |
| lineage4.2.2 0.998 T;LAM7-TUR None | |
| lineage4.2.2.2 1.000 T;LAM7-TUR None | |
| Resistance report | |
| ----------------- | |
| Drug Genotypic Resistance Mutations | |
| Rifampicin R rpoB p.His445Cys (1.00) | |
| Isoniazid R katG p.Ser315Thr (1.00) | |
| Ethambutol R embA c.-16C>T (0.98), embB p.Met306Ile (1.00) | |
| Pyrazinamide | |
| Streptomycin R gid p.Gly69Asp (1.00) | |
| Fluoroquinolones | |
| Moxifloxacin | |
| Ofloxacin | |
| Levofloxacin | |
| Ciprofloxacin | |
| Aminoglycosides | |
| Amikacin | |
| Capreomycin | |
| Kanamycin | |
| Cycloserine | |
| Ethionamide | |
| Clofazimine | |
| Para-aminosalicylic_acid | |
| Delamanid | |
| Bedaquiline | |
| Linezolid | |
| Resistance variants report | |
| ----------------- | |
| Genome Position Locus Tag Gene Variant Type Change Estimated Fraction Drug Annotation | |
| 761139 Rv0667 rpoB missense_variant p.His445Cys 1.000 rifampicin type=who_confidence|drug=rifampicin|who_confidence=Assoc w R | |
| 2155168 Rv1908c katG missense_variant p.Ser315Thr 1.000 isoniazid type=who_confidence|drug=isoniazid|who_confidence=Assoc w R | |
| 4243217 Rv3794 embA upstream_gene_variant c.-16C>T 0.980 ethambutol type=who_confidence|drug=ethambutol|who_confidence=Uncertain significance;type=who_confidence|drug=ethambutol|who_confidence=Uncertain significance | |
| 4247431 Rv3795 embB missense_variant p.Met306Ile 1.000 ethambutol type=who_confidence|drug=ethambutol|who_confidence=Assoc w R | |
| 4407997 Rv3919c gid missense_variant p.Gly69Asp 1.000 streptomycin type=who_confidence|drug=streptomycin|who_confidence=Assoc w R | |
| Other variants report | |
| --------------------- | |
| Genome Position Locus Tag Gene Variant Type Change Estimated Fraction Annotation | |
| 7362 Rv0006 gyrA missense_variant p.Glu21Gln 1.000 type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R | |
| 7585 Rv0006 gyrA missense_variant p.Ser95Thr 1.000 type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R | |
| 8688 Rv0006 gyrA missense_variant p.Ala463Ser 1.000 type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R | |
| 9304 Rv0006 gyrA missense_variant p.Gly668Asp 1.000 type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R | |
| 576077 Rv0486 mshA synonymous_variant c.730C>T 1.000 | |
| 576108 Rv0486 mshA missense_variant p.Ala254Gly 0.255 type=who_confidence|drug=ethionamide|who_confidence=Uncertain significance | |
| 761489 Rv0667 rpoB synonymous_variant c.1683G>A 1.000 | |
| 775639 Rv0676c mmpL5 missense_variant p.Ile948Val 1.000 type=who_confidence|drug=bedaquiline|who_confidence=Not assoc w R;type=who_confidence|drug=clofazimine|who_confidence=Not assoc w R | |
| 781395 Rv0682 rpsL upstream_gene_variant c.-165T>C 1.000 type=who_confidence|drug=streptomycin|who_confidence=Not assoc w R | |
| 1471659 EBG00000313325 rrs upstream_gene_variant n.-187C>T 1.000 | |
| 1917972 Rv1694 tlyA synonymous_variant c.33A>G 1.000 | |
| 2103005 Rv1854c ndh missense_variant p.Arg13Leu 1.000 | |
| 2223293 Rv1979c Rv1979c upstream_gene_variant c.-129A>G 1.000 type=who_confidence|drug=bedaquiline|who_confidence=Not assoc w R;type=who_confidence|drug=clofazimine|who_confidence=Not assoc w R | |
| 2288937 Rv2043c pncA missense_variant p.Ala102Val 1.000 type=who_confidence|drug=pyrazinamide|who_confidence=Uncertain significance | |
| 2726146 Rv2428 ahpC upstream_gene_variant c.-47_-46insT 0.970 type=who_confidence|drug=isoniazid|who_confidence=Uncertain significance | |
| 3066280 Rv2752c Rv2752c upstream_gene_variant c.-89C>T 1.000 | |
| 3086742 Rv2780 ald upstream_gene_variant c.-78A>C 1.000 | |
| 3086788 Rv2780 ald upstream_gene_variant c.-32T>C 1.000 | |
| 3339734 Rv2983 fbiD missense_variant p.Ala206Gly 0.172 | |
| 3473996 Rv3106 fprA upstream_gene_variant c.-11_-10insA 1.000 | |
| 3878641 Rv3457c rpoA upstream_gene_variant c.-134C>G 0.167 | |
| 4242643 Rv3794 embA upstream_gene_variant c.-590C>T 1.000 | |
| 4327472 Rv3854c ethA start_lost c.2T>G 1.000 | |
| 4338595 Rv3862c whiB6 upstream_gene_variant c.-75delG 1.000 type=who_confidence|drug=streptomycin|who_confidence=Not assoc w R;type=who_confidence|drug=capreomycin|who_confidence=Uncertain significance;type=who_confidence|drug=streptomycin|who_confidence=Uncertain significance;type=who_confidence|drug=capreomycin|who_confidence=Not assoc w R;type=who_confidence|drug=amikacin|who_confidence=Not assoc w R;type=who_confidence|drug=amikacin|who_confidence=Uncertain significance | |
| Coverage report | |
| --------------------- | |
| Gene Locus_Tag Cutoff Fraction | |
| gyrB Rv0005 0 0.000 | |
| gyrA Rv0006 0 0.000 | |
| fgd1 Rv0407 0 0.000 | |
| mshA Rv0486 0 0.000 | |
| ccsA Rv0529 0 0.000 | |
| rpoB Rv0667 0 0.000 | |
| rpoC Rv0668 0 0.000 | |
| mmpL5 Rv0676c 0 0.000 | |
| mmpS5 Rv0677c 0 0.000 | |
| mmpR5 Rv0678 0 0.000 | |
| rpsL Rv0682 0 0.000 | |
| rplC Rv0701 0 0.000 | |
| fbiC Rv1173 0 0.000 | |
| Rv1258c Rv1258c 0 0.000 | |
| embR Rv1267c 0 0.000 | |
| atpE Rv1305 0 0.000 | |
| rrs EBG00000313325 0 0.000 | |
| rrl EBG00000313339 0 0.000 | |
| fabG1 Rv1483 0 0.000 | |
| inhA Rv1484 0 0.000 | |
| rpsA Rv1630 0 0.000 | |
| tlyA Rv1694 0 0.000 | |
| ndh Rv1854c 0 0.000 | |
| katG Rv1908c 0 0.000 | |
| PPE35 Rv1918c 0 0.000 | |
| Rv1979c Rv1979c 0 0.000 | |
| pncA Rv2043c 0 0.000 | |
| kasA Rv2245 0 0.000 | |
| eis Rv2416c 0 0.000 | |
| ahpC Rv2428 0 0.000 | |
| folC Rv2447c 0 0.000 | |
| pepQ Rv2535c 0 0.000 | |
| ribD Rv2671 0 0.000 | |
| Rv2752c Rv2752c 0 0.000 | |
| thyX Rv2754c 0 0.000 | |
| thyA Rv2764c 0 0.000 | |
| ald Rv2780 0 0.000 | |
| fbiD Rv2983 0 0.000 | |
| Rv3083 Rv3083 0 0.000 | |
| fprA Rv3106 0 0.000 | |
| whiB7 Rv3197A 0 0.000 | |
| Rv3236c Rv3236c 0 0.000 | |
| fbiA Rv3261 0 0.000 | |
| fbiB Rv3262 0 0.000 | |
| alr Rv3423c 0 0.000 | |
| rpoA Rv3457c 0 0.000 | |
| ddn Rv3547 0 0.000 | |
| clpC1 Rv3596c 0 0.000 | |
| panD Rv3601c 0 0.000 | |
| embC Rv3793 0 0.000 | |
| embA Rv3794 0 0.000 | |
| embB Rv3795 0 0.000 | |
| aftB Rv3805c 0 0.000 | |
| ubiA Rv3806c 0 0.000 | |
| ethA Rv3854c 0 0.000 | |
| ethR Rv3855 0 0.000 | |
| whiB6 Rv3862c 0 0.000 | |
| gid Rv3919c 0 0.000 | |
| Missing positions report | |
| --------------------- | |
| Gene Locus_Tag Position Variants Drugs | |
| rrs EBG00000313325 1472644 n.799C>T streptomycin | |
| rrs EBG00000313325 1472723 n.878G>A streptomycin | |
| rrs EBG00000313325 1472733 n.888G>A streptomycin | |
| rrs EBG00000313325 1472750 n.905C>A,n.905C>G streptomycin | |
| rrs EBG00000313325 1472751 n.906A>G streptomycin | |
| rrs EBG00000313325 1472752 n.907A>T,n.907A>C streptomycin | |
| rrs EBG00000313325 1472753 n.908A>G streptomycin | |
| Analysis pipeline specifications | |
| -------------------------------- | |
| Pipeline version: 4.4.2 | |
| Database version: tbdb_0599ccd_Jody Phelan <jody.phelan@lshtm.ac.uk>_Mon Mar 27 07:30:48 2023 +0100 | |
| Analysis Program | |
| Mapping /cromwell_root/fc-a1a6f6f6-9b6b-4f91-b4d5-80c194dfe383/submissions/22704433-0f79-46a9-9054-77282ef7c4e5/myco/5e435175-60f1-48dc-9f56-ebf94bcb640d/call-decontam_each_sample/shard-0/cacheCopy/SAMEA11744634_1.decontam.fq.gz | |
| Variant calling freebayes | |
| Citation | |
| -------- | |
| Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from | |
| whole-genome sequences. Genome Medicine 7, 51. 2015 | |
| Phelan, JE. et al. Integrating informatics tools and portable sequencing | |
| technology for rapid detection of resistance to anti-tuberculous drugs. | |
| Genome Medicine 11, 41. 2019 |
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