TB-Profiler result

Run: SRR25827740
Summary

Run ID: SRR25827740

Sample name:

Date: 2024-10-04T22:39:41.647411

Number of reads: 9981030

Percentage reads mapped: 98.87

Median coverage: 329.0

Strain: lineage2.2.1.1;lineage3;lineage4

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
lineage3 East-African-Indian RD750 0.22
lineage2 East-Asian RD105 0.66
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.67
lineage4 Euro-American None 0.1
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.16
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Cys Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg 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 thyA p.Thr22Ala Mutation from literature
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 0.52 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Cys missense_variant 0.98 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoC 764841 p.Ile491Thr missense_variant 0.2 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.54 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.14 pyrazinamide Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.14 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.19 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.38 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
gyrB 6963 p.Arg575His missense_variant 0.26 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 491290 p.Val170Met missense_variant 0.18 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.89 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.71 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.29 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.72 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.66 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.24 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.21 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 764363 p.Gly332Ser missense_variant 0.14 rifampicin Uncertain significance
rpoC 764817 p.Val483Ala missense_variant 0.37 rifampicin Uncertain significance
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 0.92 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776181 p.Asp767Thr missense_variant 0.26 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253956 p.Gln193His missense_variant 0.19 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.6 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.65 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.91 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.92 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 2289365 c.-125delC upstream_gene_variant 0.32 pyrazinamide
eis 2714846 p.Val163Ile missense_variant 0.16 kanamycin Not assoc w R
amikacin Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.21 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.29 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
pepQ 2859931 p.Leu163Arg missense_variant 0.15 bedaquiline
clofazimine
thyX 3067949 c.-4C>T upstream_gene_variant 0.26 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.64 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.73 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640211 c.-332T>G upstream_gene_variant 0.26 pretomanid
delamanid
clofazimine
alr 3841578 c.-158G>A upstream_gene_variant 0.25 cycloserine
alr 3841590 c.-170G>A upstream_gene_variant 0.25 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.2 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240827 p.Ala322Gly missense_variant 0.23 ethambutol
embC 4241022 p.Ala387Val missense_variant 0.18 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.19 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.67 ethambutol Not assoc w R
embA 4245303 c.2071C>T synonymous_variant 0.2 ethambutol Not assoc w R - Interim
embA 4245835 p.Leu868Arg missense_variant 0.17 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.29 ethambutol
embB 4248115 c.1602C>T synonymous_variant 0.14 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.34 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.48 ethambutol Not assoc w R
aftB 4268719 p.Asn40Asp missense_variant 0.21 ethambutol Uncertain significance
ethA 4327082 p.Cys131Tyr missense_variant 0.27 ethionamide Uncertain significance
whiB6 4338292 p.Ala77Val missense_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 4407588 c.615A>G synonymous_variant 0.9 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.19 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.67 streptomycin Not assoc w R
gid 4408070 p.Trp45Arg missense_variant 0.22 streptomycin Uncertain significance