TB-Profiler result

Run: ERR2987806
Summary

Run ID: ERR2987806

Sample name:

Date: 2024-10-03T17:45:56.568619

Number of reads: 33643977

Percentage reads mapped: 98.96

Median coverage: 268.0

Strain: lineage4.2.1.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 1.0
lineage4.2.1 Euro-American (TUR) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776536 p.Lys649Gln missense_variant 1.0 bedaquiline
clofazimine
mmpL5 777451 p.Val344Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.59 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.22 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170813 c.-201G>C upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3064701 p.Phe497Leu missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840696 p.Ala242Val missense_variant 0.57 cycloserine
ddn 3987092 p.Glu83Asp missense_variant 1.0 pretomanid
delamanid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
gid 4408213 c.-11C>T upstream_gene_variant 1.0 streptomycin Uncertain significance