TB-Profiler result

Run: ERR4829916
Summary

Run ID: ERR4829916

Sample name:

Date: 2024-10-03T15:42:55.485361

Number of reads: 3333310

Percentage reads mapped: 98.49

Median coverage: 103.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.24
lineage4.1.2 Euro-American None 0.24
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.24
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.78
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
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
rpoB 761101 p.Gln432Pro missense_variant 0.25 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.22 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.2 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
dnaA 371 p.Pro124Leu missense_variant 0.87 isoniazid Not assoc w R
gyrB 6639 p.Ala467Val missense_variant 0.18 levofloxacin Uncertain significance
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 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.32 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.23 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.17 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.22 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.3 rifampicin Not assoc w R
rpoC 766085 p.Pro906Ala missense_variant 0.72 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777820 c.661C>T synonymous_variant 0.26 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
atpE 1460992 c.-53A>C upstream_gene_variant 0.81 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.8 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.21 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2221897 p.Val423Ala missense_variant 0.83 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 2518076 c.-39C>T upstream_gene_variant 0.26 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.26 cycloserine
whiB7 3568971 c.-292G>A upstream_gene_variant 0.16 kanamycin
amikacin
streptomycin
mtrB 3625065 p.Met517Leu missense_variant 0.28 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.8 cycloserine
rpoA 3878432 c.76C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.33 ethambutol Not assoc w R
embC 4239655 c.-208C>T upstream_gene_variant 0.75 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.24 ethambutol Not assoc w R
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 0.24 kanamycin
capreomycin
amikacin
gid 4407970 p.Pro78Gln missense_variant 0.21 streptomycin Uncertain significance