TB-Profiler result

Run: ERR4799370
Summary

Run ID: ERR4799370

Sample name:

Date: 2024-03-27T06:02:23.745938

Number of reads: 2611033

Percentage reads mapped: 99.66

Median coverage: 73.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.37
lineage2.2 East-Asian (Beijing) RD105;RD207 0.37
lineage4 Euro-American None 0.6
lineage4.8 Euro-American (mainly T) RD219 0.63
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
p.Ala264Thr Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.67 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
gyrA 7582 p.Asp94Ala missense_variant 0.33 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid Assoc w R High-level resistance
katG 2155322 p.Ala264Thr missense_variant 0.67 isoniazid Uncertain significance Mutation from literature
pncA 2289162 p.Leu27Pro missense_variant 0.37 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.32 ethambutol Assoc w R
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 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.41 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.24 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.6 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.3 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.69 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 766488 p.Pro1040Arg missense_variant 0.24 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.44 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.45 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.31 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.33 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.37 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.3 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.65 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.65 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.36 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.33 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.33 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.66 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.34 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.38 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 0.65 pyrazinamide Not assoc w R
embC 4240061 p.Phe67Val missense_variant 0.56 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.33 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.4 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.23 ethionamide Uncertain significance
ethA 4327065 p.Cys137Arg missense_variant 0.17 ethionamide Uncertain significance
ethA 4327436 p.Gly13Val missense_variant 0.37 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.42 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.36 streptomycin Not assoc w R
gid 4407925 p.Pro93Leu missense_variant 0.62 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.4 streptomycin Not assoc w R