TB-Profiler result

Run: SRR25827430
Summary

Run ID: SRR25827430

Sample name:

Date: 2024-10-04T21:17:01.351909

Number of reads: 1668731

Percentage reads mapped: 98.77

Median coverage: 56.5

Strain: lineage2.2.1;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
lineage2 East-Asian RD105 0.77
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.78
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.09
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 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 embA c.-16C>T Uncertain significance Mutation from literature
c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gly406Ser Assoc w R
pyrazinamide pncA c.391dupG Assoc w R
p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Ala 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 gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.449_481delGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGA Mutation from literature
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
gyrA 7570 p.Ala90Val missense_variant 0.2 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.Asp94Ala missense_variant 0.31 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 0.41 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.44 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)
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.2 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.35 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.33 ethambutol Uncertain significance Mutation from literature
embA 4243222 c.-11C>A upstream_gene_variant 0.22 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.57 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.36 ethambutol Assoc w R
ethA 4326992 c.449_481delGATTCGCCGGCTCGGAGGATTTCGTCGGGCCGA disruptive_inframe_deletion 0.35 ethionamide 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 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.15 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.98 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.44 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.89 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 764723 p.Phe452Leu missense_variant 0.33 rifampicin Uncertain significance
rpoC 765862 p.Phe831Leu missense_variant 0.18 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.29 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 0.86 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.48 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.13 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.74 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 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303326 c.396C>T synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.89 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
atpE 1461153 p.Ser37Ala missense_variant 0.27 bedaquiline Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.77 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.9 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 0.89 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.93 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.18 pyrazinamide Not assoc w R
Rv1979c 2222357 p.Thr270Ala missense_variant 0.22 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.8 cycloserine
ald 3086821 p.Met1? start_lost 0.16 cycloserine
Rv3083 3448936 p.Tyr145Asp missense_variant 0.17 ethionamide Uncertain significance
whiB7 3568555 p.Leu42Pro missense_variant 0.45 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568854 c.-176delG upstream_gene_variant 0.42 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.33 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.9 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.87 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.13 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 0.77 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.17 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.97 ethambutol Not assoc w R
ubiA 4269296 p.Met180Val missense_variant 0.16 ethambutol Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.4 ethionamide 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 0.94 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.9 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.24 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.82 streptomycin Not assoc w R