TB-Profiler result

Run: SRR13312530
Summary

Run ID: SRR13312530

Sample name:

Date: 2024-10-04T18:09:23.197174

Number of reads: 17813446

Percentage reads mapped: 99.51

Median coverage: 397.0

Strain: lineage4.2.1;lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 0.14
lineage4.2 Euro-American None 0.85
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.88
lineage4.3.3 Euro-American (LAM) RD115 0.14
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine ald c.436_437dupGC Mutation from literature
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
gyrA 7582 p.Asp94Ala missense_variant 0.1 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.14 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.11 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.13 pyrazinamide Assoc w R
eis 2715346 c.-14C>T upstream_gene_variant 0.15 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
ald 3087252 c.436_437dupGC frameshift_variant 0.12 cycloserine Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.12 ethambutol 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 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 8040 p.Gly247Ser missense_variant 0.12 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 491247 c.465C>T synonymous_variant 0.87 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv0565c 656125 c.1345dupG frameshift_variant 0.14 ethionamide Uncertain significance
Rv0565c 656832 c.639G>A synonymous_variant 0.16 ethionamide Not assoc w R - Interim
rpoB 761032 p.Gln409Arg missense_variant 0.15 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.13 rifampicin Not assoc w R
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
rplC 800204 c.-605T>C upstream_gene_variant 0.87 linezolid
fbiC 1302901 c.-30G>T upstream_gene_variant 0.85 pretomanid
delamanid
clofazimine
fbiC 1303095 c.165G>A synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476222 n.2565A>C non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.12 pyrazinamide 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
bacA 2063685 c.1044G>A synonymous_variant 0.87 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.86 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.15 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.86 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726142 c.-51G>A upstream_gene_variant 0.13 isoniazid Uncertain significance
folC 2746340 p.Ala420Val missense_variant 0.12 para-aminosalicylic_acid
ribD 2987502 p.Gly222Ser missense_variant 0.17 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.14 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.84 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612696 p.Arg141Gly missense_variant 0.84 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.15 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.85 ethambutol Not assoc w R - Interim
ethA 4326593 p.Cys294Tyr missense_variant 0.14 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.89 ethionamide
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 4408156 p.Leu16Arg missense_variant 0.17 streptomycin Not assoc w R