TB-Profiler result

Run: ERR4972575

Summary

Run ID: ERR4972575

Sample name:

Date: 2024-03-24T16:08:44.846070

Number of reads: 4708326

Percentage reads mapped: 99.58

Median coverage: 160.0

Strain: lineage4.3.3;lineage4.4.1.1

Spoligotype:

Drug-resistance: 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 0.41
lineage4.4.1 Euro-American (S-type) None 0.64
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.63
lineage4.3.3 Euro-American (LAM) RD115 0.37
lineage4.4 Euro-American None 0.64
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.314dupG Assoc w R
p.Val9Ala Uncertain significance Mutation from literature
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1484G>T Assoc w R
capreomycin rrs n.1484G>T Assoc w R
kanamycin rrs n.1484G>T Assoc w R
cycloserine
ethionamide ethA c.671delA Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 7570 p.Ala90Val missense_variant 0.43 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 761110 p.Asp435Val missense_variant 0.66 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.34 rifampicin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.46 linezolid Assoc w R
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.38 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 2288927 c.314dupG frameshift_variant 0.38 pyrazinamide Assoc w R
pncA 2289216 p.Val9Ala missense_variant 0.62 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4326802 c.671delA frameshift_variant 0.39 ethionamide 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
gyrB 6825 p.Leu529Pro missense_variant 0.4 levofloxacin
moxifloxacin
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 7677 p.Ala126Pro missense_variant 0.57 levofloxacin Uncertain significance
moxifloxacin
gyrA 8040 p.Gly247Ser missense_variant 0.34 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 576108 p.Ala254Gly missense_variant 0.22 ethionamide
isoniazid
ccsA 620290 p.Tyr134His missense_variant 0.35 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
rpoC 764918 p.Val517Leu missense_variant 0.34 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.43 rifampicin Not assoc w R
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
rrs 1473106 n.1261A>G non_coding_transcript_exon_variant 0.59 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
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
ndh 2102990 p.Val18Ala missense_variant 0.67 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2167870 p.Gly915* stop_gained 0.3 pyrazinamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.53 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.31 isoniazid
folC 2746603 c.996C>T synonymous_variant 0.68 para-aminosalicylic_acid
Rv2680 2996145 p.Glu14Gly missense_variant 0.33 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.38 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
Rv3083 3449854 p.Met451Val missense_variant 0.33 ethionamide Uncertain significance
Rv3236c 3612665 p.Val151Ala missense_variant 0.61 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.68 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327416 p.Ala20Thr missense_variant 0.57 ethionamide
whiB6 4338594 c.-73T>A upstream_gene_variant 0.44 capreomycin
amikacin
kanamycin
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 4407854 p.Gly117Arg missense_variant 0.65 streptomycin Uncertain significance
gid 4408096 p.Val36Ala missense_variant 0.35 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.39 streptomycin Not assoc w R
gid 4408233 c.-31A>G upstream_gene_variant 0.35 streptomycin