TB-Profiler result

Run: SRR29096344
Summary

Run ID: SRR29096344

Sample name:

Date: 2025-02-11T20:29:31.199816

Number of reads: 1713594

Percentage reads mapped: 99.59

Median coverage: 52.0

Strain: lineage2.2.2;lineage4.3.3

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 0.86
lineage2 East-Asian RD105 0.09
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.07
lineage2.2 East-Asian (Beijing) RD105;RD207 0.06
lineage4 Euro-American None 0.9
lineage4.3.3 Euro-American (LAM) RD115 0.85
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 inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A. 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 embB p.Met306Ile Assoc w R
pyrazinamide pncA c.517dupG Assoc w R
c.389delT Assoc w R
streptomycin gid c.160_290del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>A Assoc w R - Interim Alias fabG1_c.-8T>A
ethA c.-11A>G Uncertain significance Mutation from literature
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 761155 p.Ser450Leu missense_variant 0.93 rifampicin Assoc w R
inhA 1673432 c.-770T>A upstream_gene_variant 0.88 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>A
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>A. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.26 pyrazinamide Assoc w R
pncA 2288852 c.389delT frameshift_variant 0.83 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4327484 c.-11A>G upstream_gene_variant 0.78 ethionamide Uncertain significance Mutation from literature
gid 4407912 c.160_290del frameshift_variant 0.92 streptomycin 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 0.98 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 8040 p.Gly247Ser missense_variant 0.88 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
fgd1 491742 c.960T>C synonymous_variant 0.26 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.78 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
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 0.84 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
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
Rv1979c 2221939 p.Arg409Gln missense_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223051 p.Glu38Asp missense_variant 0.85 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.85 isoniazid
Rv2752c 3065824 p.Pro123Leu missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.79 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841356 p.Ser22Leu missense_variant 0.83 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.85 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269742 p.Leu31Pro missense_variant 0.84 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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.21 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.16 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.88 streptomycin Not assoc w R