TB-Profiler result

Run: SRR1172365
Summary

Run ID: SRR1172365

Sample name:

Date: 2024-04-16T08:01:38.608084

Number of reads: 995136

Percentage reads mapped: 98.11

Median coverage: 22.0

Strain: lineage4.3.4.2.1;lineage4.4.1.1.1

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 0.5
lineage4.4.1.1.1 Euro-American None 0.52
lineage4.4.1 Euro-American (S-type) None 0.51
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.56
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.57
lineage4.3.4 Euro-American (LAM) RD174 0.52
lineage4.4 Euro-American None 0.49
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Leu Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Ala Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
rpoB 761140 p.His445Leu missense_variant 0.56 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.47 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.46 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.31 kanamycin Assoc w R
amikacin Assoc w R
capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.55 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.5 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.58 ethambutol Uncertain significance Mutation from literature
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 6140 p.Val301Leu missense_variant 0.64 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575538 p.Asp64Gly missense_variant 0.57 ethionamide
isoniazid
rpoC 764744 p.Arg459Trp missense_variant 0.52 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ser missense_variant 0.45 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853674 c.69G>A synonymous_variant 0.48 linezolid Not assoc w R - Interim
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
ndh 2102990 p.Val18Ala missense_variant 0.41 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.43 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.38 para-aminosalicylic_acid
Rv2752c 3064993 p.Trp400* stop_gained 0.64 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.68 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339287 p.Arg57Leu missense_variant 0.53 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.64 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.48 pyrazinamide Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.74 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.52 streptomycin Not assoc w R