TB-Profiler result

Run: SRR25827617
Summary

Run ID: SRR25827617

Sample name:

Date: 2024-04-16T01:46:58.493305

Number of reads: 5548222

Percentage reads mapped: 99.42

Median coverage: 62.0

Strain: lineage1.2.2.2;lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: 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 0.28
lineage1.2.2 Indo-Oceanic RD239 0.24
lineage2 East-Asian RD105 0.46
lineage1.2.2.2 Indo-Oceanic RD239 0.15
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.47
lineage2.2 East-Asian (Beijing) RD105;RD207 0.48
lineage1 Indo-Oceanic RD239 0.2
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.517C>T 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 tlyA c.589dupG Assoc w R
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.139dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.139dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
linezolid rplC p.Cys154Arg Assoc w R
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 0.58 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin Assoc w R
mmpR5 779127 c.139dupG frameshift_variant 0.29 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.4 linezolid Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.37 streptomycin Assoc w R
tlyA 1918524 c.589dupG frameshift_variant 0.33 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.61 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
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 8452 p.Ala384Val missense_variant 0.35 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.3 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
Rv0010c 13298 p.Ile87Met missense_variant 0.17 isoniazid Not assoc w R
fgd1 490977 c.195C>G synonymous_variant 0.45 clofazimine Not assoc w R - Interim
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.36 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.47 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.65 ethionamide Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.27 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.24 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.31 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.31 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.21 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416814 c.534G>A synonymous_variant 0.15 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.37 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.62 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.5 linezolid 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 2102240 p.Arg268His missense_variant 0.22 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2102359 c.683delT frameshift_variant 0.34 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.21 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288683 c.559T>G stop_lost&splice_region_variant 0.18 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.26 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.23 isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.3 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.31 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.44 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.42 clofazimine
pretomanid
delamanid
clpC1 4040517 p.Val63Ala missense_variant 0.38 pyrazinamide Not assoc w R - Interim
panD 4044023 c.259C>T synonymous_variant 0.26 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.19 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.16 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.5 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.27 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 0.33 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.26 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.4 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.55 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.2 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.26 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.45 ethionamide Not assoc w R - Interim
whiB6 4338203 p.Arg107Cys missense_variant 0.3 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.88 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.39 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.39 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.44 streptomycin Not assoc w R