TB-Profiler result

Run: SRR18593215
Summary

Run ID: SRR18593215

Sample name:

Date: 2024-10-04T15:21:40.690500

Number of reads: 4559494

Percentage reads mapped: 97.58

Median coverage: 127.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.96
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
p.Ser450Trp Assoc w R
isoniazid katG p.Ser315Arg Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
p.Gln497Lys Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide
streptomycin rrs n.906A>G Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Asp89Asn Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Asp89Asn Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.126_127dupGG Assoc w R
kanamycin
cycloserine
ethionamide ethA c.788_798delTGTTCCTGAGC Assoc w R
c.752dupG Assoc w R
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
gyrB 6738 p.Thr500Asn missense_variant 0.73 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7566 p.Asp89Asn missense_variant 0.89 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)
gyrA 7582 p.Asp94Gly missense_variant 0.11 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 0.88 rifampicin Assoc w R
rpoB 761155 p.Ser450Trp missense_variant 0.12 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance Mutation from literature
tlyA 1918064 c.126_127dupGG frameshift_variant 0.14 capreomycin Assoc w R
katG 2155169 p.Ser315Arg missense_variant 0.83 isoniazid Assoc w R High-level resistance
embB 4247574 p.Asp354Ala missense_variant 0.11 ethambutol Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.78 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.86 ethambutol Uncertain significance Mutation from literature
ethA 4326675 c.788_798delTGTTCCTGAGC frameshift_variant 0.85 ethionamide Assoc w R
ethA 4326721 c.752dupG frameshift_variant 0.15 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 6091 c.852G>A synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 574518 c.-830A>G upstream_gene_variant 0.98 isoniazid
ethionamide
rpoB 761231 c.1425C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
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 1253847 p.Ala230Thr missense_variant 0.89 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.98 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1674283 p.Val28Leu missense_variant 0.98 isoniazid Uncertain significance
ethionamide
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
katG 2155627 p.Ala162Glu missense_variant 0.11 isoniazid Uncertain significance
katG 2156419 c.-308C>A upstream_gene_variant 0.84 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288832 p.His137Leu missense_variant 0.12 pyrazinamide
pncA 2289040 c.187_201dupGACTATTCCTCGTCG conservative_inframe_insertion 0.76 pyrazinamide
ahpC 2726142 c.-51G>A upstream_gene_variant 0.17 isoniazid Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.96 capreomycin
Rv2752c 3065938 p.Asp85Gly missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086966 p.Asp49Glu missense_variant 0.98 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.98 ethionamide Uncertain significance
Rv3236c 3612047 p.Ala357Val missense_variant 0.99 pyrazinamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326505 c.969C>G synonymous_variant 0.95 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408139 p.Tyr22Asn missense_variant 0.89 streptomycin Uncertain significance