TB-Profiler result

Run: ERR11082159
Summary

Run ID: ERR11082159

Sample name:

Date: 2024-10-04T02:50:35.491123

Number of reads: 4298785

Percentage reads mapped: 99.63

Median coverage: 132.0

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 0.5
lineage4.1.2 Euro-American None 0.49
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.49
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.51
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Phe424Val Uncertain significance Mutation from literature
p.Leu430Pro Assoc w R
p.Ser450Trp 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
streptomycin gid c.200_214delATATCGGTAGCGGAG Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA p.Tyr438* 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
rpoB 761076 p.Phe424Val missense_variant 0.46 rifampicin Uncertain significance Mutation from literature
rpoB 761095 p.Leu430Pro missense_variant 0.44 rifampicin Assoc w R
rpoB 761155 p.Ser450Trp missense_variant 0.48 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.52 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.55 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.58 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.53 ethambutol Assoc w R
ethA 4326160 p.Tyr438* stop_gained 0.47 ethionamide Assoc w R
gid 4407988 c.200_214delATATCGGTAGCGGAG disruptive_inframe_deletion 0.39 streptomycin Mutation from literature
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 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.5 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.61 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.4 ethionamide Uncertain significance
rpoB 759627 c.-180A>C upstream_gene_variant 0.43 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.43 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.47 rifampicin Not assoc w R
rpoC 766744 p.Gln1125His missense_variant 0.5 rifampicin Uncertain significance
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 800202 c.-607G>C upstream_gene_variant 0.48 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.54 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853987 p.Ile128Leu missense_variant 0.55 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.46 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154799 p.Trp438Leu missense_variant 0.44 isoniazid
PPE35 2169503 c.1109delG frameshift_variant 0.39 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289109 p.Val45Met missense_variant 0.5 pyrazinamide Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.39 isoniazid
Rv2681 2997575 c.837T>C synonymous_variant 0.44 capreomycin Not assoc w R - Interim
Rv2752c 3067180 c.-989C>A upstream_gene_variant 0.51 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.51 cycloserine
fbiD 3339324 c.207G>T synonymous_variant 0.44 pretomanid
delamanid
clofazimine
mtrB 3625065 p.Met517Leu missense_variant 0.39 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.49 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.42 ethambutol Not assoc w R
embA 4243228 c.-5G>A upstream_gene_variant 0.51 ethambutol 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 0.54 kanamycin
capreomycin
amikacin