TB-Profiler result

Run: ERR164021
Summary

Run ID: ERR164021

Sample name:

Date: 2024-04-15T23:33:34.689379

Number of reads: 8921572

Percentage reads mapped: 94.99

Median coverage: 195.0

Strain: lineage1.2.2.2;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.68
lineage1.2.2 Indo-Oceanic RD239 0.29
lineage1.2.2.2 Indo-Oceanic RD239 0.31
lineage4 Euro-American None 0.69
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.7
lineage1 Indo-Oceanic RD239 0.32
lineage4.3.4 Euro-American (LAM) RD174 0.69
lineage4.3.4.2 Euro-American (LAM) RD174 0.7
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin rrs n.514A>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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
rpoB 761139 p.His445Asn missense_variant 0.27 rifampicin Assoc w R
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 0.23 streptomycin Uncertain significance Mutation from literature
inhA 1674481 p.Ser94Ala missense_variant 0.28 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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
gyrB 5075 c.-165C>T upstream_gene_variant 0.27 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.27 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
Rv0010c 13298 p.Ile87Met missense_variant 0.29 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.17 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.16 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.26 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.25 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.19 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.33 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.3 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.27 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.73 rifampicin Not assoc w R
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 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777017 c.1464C>T synonymous_variant 0.65 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.28 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.23 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.18 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.24 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.24 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.29 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.27 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.29 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.26 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.29 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.32 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.2 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.28 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.74 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.24 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.66 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.36 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626158 c.456C>T synonymous_variant 0.26 bedaquiline
rifampicin
mtrB 3626467 c.147G>A synonymous_variant 0.27 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.67 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.76 pyrazinamide Not assoc w R
clpC1 4038328 p.Glu793Gln missense_variant 0.26 pyrazinamide Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.3 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.3 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.36 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.3 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.27 ethambutol Not assoc w R
embC 4242559 c.2697G>A synonymous_variant 0.4 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.28 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.34 ethambutol Not assoc w R
embB 4246979 p.Gly156Cys missense_variant 0.35 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.32 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.2 ethambutol Uncertain significance
ubiA 4269162 p.Leu224Phe missense_variant 0.29 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.36 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.3 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.27 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.33 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.27 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.25 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.29 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.26 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.72 streptomycin Not assoc w R