TB-Profiler result

Run: SAMN11603930
Summary

Run ID: SAMN11603930

Sample name:

Date: 2024-04-15T13:45:05.226318

Number of reads: 95700042

Percentage reads mapped: 99.38

Median coverage: 2772.0

Strain: lineage3.1.2;lineage4.9

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
lineage3 East-African-Indian RD750 0.55
lineage3.1.2 East-African-Indian RD750 0.13
lineage4 Euro-American None 0.18
lineage4.9 Euro-American (H37Rv-like) None 0.07
lineage3.1 East-African-Indian RD750 0.12
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Leu172Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 7582 p.Asp94Gly missense_variant 0.32 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Tyr missense_variant 0.14 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.44 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.19 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.16 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.59 isoniazid Assoc w R High-level resistance
pncA 2288727 p.Leu172Pro missense_variant 0.12 pyrazinamide Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.13 streptomycin 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 6112 p.Met291Ile missense_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6446 p.Ala403Ser missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.24 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.84 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576108 p.Ala254Gly missense_variant 0.16 ethionamide
isoniazid
Rv0565c 657081 c.390G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.28 ethionamide
rpoB 759746 c.-61C>T upstream_gene_variant 0.48 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.52 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 766582 c.3213C>A synonymous_variant 0.24 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 0.81 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.82 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.24 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.94 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 0.18 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064596 p.Thr45Ala missense_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.83 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.16 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.22 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
pncA 2288743 p.Thr167Pro missense_variant 0.11 pyrazinamide Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.54 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.27 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.51 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.5 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2784617 c.-575T>C upstream_gene_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.89 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.1 ethionamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.12 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.24 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.91 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.22 cycloserine
clpC1 4040062 p.Ile215Val missense_variant 0.1 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.58 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.25 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
glpK 4138622 c.1134C>T synonymous_variant 0.54 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.19 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.53 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.94 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsCA frameshift_variant&missense_variant 0.27 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.16 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.28 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.22 ethambutol Not assoc w R
ethA 4327346 p.Gly43Val missense_variant 0.15 ethionamide Uncertain significance
whiB6 4338424 p.Val33Gly missense_variant 0.12 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.95 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.81 streptomycin Not assoc w R