TB-Profiler result

Run: SRR1165643
Summary

Run ID: SRR1165643

Sample name:

Date: 2024-10-03T22:29:23.671711

Number of reads: 4726374

Percentage reads mapped: 99.23

Median coverage: 111.0

Strain: lineage4.3.4.2.1;lineage4.4.1.1.1

Spoligotype:

Drug-resistance: HR-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 0.58
lineage4.4.1.1.1 Euro-American None 0.33
lineage4.4.1 Euro-American (S-type) None 0.35
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.37
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.63
lineage4.3.4 Euro-American (LAM) RD174 0.65
lineage4.3.4.2 Euro-American (LAM) RD174 0.63
lineage4.4 Euro-American None 0.3
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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 pncA p.Tyr34Asp Assoc w R
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
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289142 p.Tyr34Asp missense_variant 0.18 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.18 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.53 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.72 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
dnaA 1391 p.Gln464Arg missense_variant 0.6 isoniazid Uncertain significance
gyrB 6140 p.Val301Leu missense_variant 0.66 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
rpoC 764744 p.Arg459Trp missense_variant 0.61 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 765494 p.Val709Leu missense_variant 0.61 rifampicin
rpoC 766487 p.Pro1040Ser missense_variant 0.33 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
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
ndh 2102990 p.Val18Ala missense_variant 0.31 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.33 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2986827 c.-12G>A upstream_gene_variant 0.39 para-aminosalicylic_acid
Rv2752c 3064993 p.Trp400* stop_gained 0.48 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.62 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.77 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.66 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.56 pyrazinamide Not assoc w R
ubiA 4269308 p.Phe176Leu missense_variant 0.4 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407714 p.Lys163Asn missense_variant 0.55 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.5 streptomycin Not assoc w R