TB-Profiler result

Run: ERR1035070
Summary

Run ID: ERR1035070

Sample name:

Date: 2024-10-04T10:42:01.625826

Number of reads: 8473348

Percentage reads mapped: 99.5

Median coverage: 182.0

Strain: lineage4.3.2.1;lineage4.4.1.1

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 0.53
lineage4.3.2 Euro-American (LAM) None 0.52
lineage4.3.2.1 Euro-American (LAM) RD761 0.53
lineage4.4.1 Euro-American (S-type) None 0.49
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.5
lineage4.4 Euro-American None 0.49
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Val130Ala Mutation from literature
p.Leu85Pro Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Trp missense_variant 0.48 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.52 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288853 p.Val130Ala missense_variant 0.47 pyrazinamide Mutation from literature
pncA 2288988 p.Leu85Pro missense_variant 0.51 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.53 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.46 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.49 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
gyrB 5520 p.Pro94Leu missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7222 c.1983C>T synonymous_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 9138 p.Gln613Glu missense_variant 0.45 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 576672 c.1327_1328dupCG frameshift_variant 0.34 isoniazid Uncertain significance
ethionamide Uncertain significance
rpoB 762793 c.2993_2998dupCCGACG disruptive_inframe_insertion 0.36 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 0.55 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 777416 c.1065G>T synonymous_variant 0.56 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpL5 778510 c.-30T>C upstream_gene_variant 0.5 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304345 p.Asp472Ala missense_variant 0.51 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.49 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
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 0.46 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2168479 p.Thr712Pro missense_variant 0.51 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.55 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3064552 c.1639delC frameshift_variant 0.52 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.48 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086944 c.126dupC frameshift_variant 0.43 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
Rv3083 3449108 p.Gly202Asp missense_variant 0.5 ethionamide Uncertain significance
whiB7 3568779 c.-100T>C upstream_gene_variant 0.43 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.42 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.47 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327059 p.Gly139Cys missense_variant 0.47 ethionamide 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
gid 4407760 p.Trp148Ser missense_variant 0.48 streptomycin
gid 4408156 p.Leu16Arg missense_variant 0.44 streptomycin Not assoc w R