TB-Profiler result

Run: SRR7652980
Summary

Run ID: SRR7652980

Sample name:

Date: 2024-10-04T19:46:32.231165

Number of reads: 7737251

Percentage reads mapped: 99.61

Median coverage: 233.0

Strain: lineage2.2.1;lineage4.1.2.1

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
lineage2 East-Asian RD105 0.83
lineage4.1 Euro-American None 0.17
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.18
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.82
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.17
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Asp435Ile Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA c.407_408insG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461Asn Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Asp461Asn Assoc w R
gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.697_698dupCC Assoc w R
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Arg207Gly 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 6620 p.Asp461Asn missense_variant 0.86 levofloxacin Assoc w R
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.17 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761095 p.Leu430Pro missense_variant 0.82 rifampicin Assoc w R
rpoB 761109 p.Asp435Ile missense_variant 0.83 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.13 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
tlyA 1918634 c.697_698dupCC frameshift_variant 0.15 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288834 c.407_408insG frameshift_variant 0.89 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.16 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.85 ethambutol Assoc w R
ethA 4326855 p.Arg207Gly missense_variant 0.81 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.18 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.83 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.15 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.85 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.86 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.85 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.84 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.14 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.17 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.86 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.16 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.81 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 776100 p.Thr794Ile missense_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.88 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472906 n.1061T>C non_coding_transcript_exon_variant 0.12 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
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
katG 2154724 p.Arg463Leu missense_variant 0.83 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.88 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
pncA 2288760 p.Ala161Gly missense_variant 0.14 pyrazinamide Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.21 isoniazid
thyA 3073715 p.Pro253Ala missense_variant 0.82 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.77 pyrazinamide Not assoc w R - Interim
Rv3236c 3613286 c.-170C>G upstream_gene_variant 0.15 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.82 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640340 c.-203G>A upstream_gene_variant 0.84 pretomanid
delamanid
clofazimine
embC 4239298 c.-565C>T upstream_gene_variant 0.17 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 0.2 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.79 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.83 ethambutol Not assoc w R
ethA 4327424 p.Val17Gly missense_variant 0.16 ethionamide
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 4407588 c.615A>G synonymous_variant 0.85 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.86 streptomycin Not assoc w R
gid 4407973 p.Val77Ala missense_variant 0.15 streptomycin Uncertain significance