TB-Profiler result

Run: SRR1049972
Summary

Run ID: SRR1049972

Sample name:

Date: 2024-04-15T04:01:09.191182

Number of reads: 7783124

Percentage reads mapped: 98.9

Median coverage: 151.0

Strain: lineage4.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.99
lineage4.1 Euro-American None 1.0
lineage4 Euro-American None 1.0
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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.Gln497Arg Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
streptomycin gid c.-970_*46024del Assoc w R
c.669_*34930del Assoc w R
p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA c.-24907_*22804del Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid fbiA c.-19640_*6030del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-14933_*20180del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-5543_*2480del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-4218_*18279del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-32360_*15783del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-20244_*23163del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-18495_*18954del Assoc w R - Interim Confers DLM-PMD cross-resistance
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.93 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2289081 p.Pro54Leu missense_variant 0.98 pyrazinamide Assoc w R
fbiA 3620902 c.-19640_*6030del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3625609 c.-14933_*20180del transcript_ablation 0.92 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3634999 c.-5543_*2480del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3636324 c.-4218_*18279del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3954483 c.-32360_*15783del transcript_ablation 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3966599 c.-20244_*23163del transcript_ablation 0.93 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3968348 c.-18495_*18954del transcript_ablation 0.9 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol Assoc w R
ethA 4303199 c.-24907_*22804del transcript_ablation 0.93 ethionamide Assoc w R
gid 4361503 c.-970_*46024del transcript_ablation 0.92 streptomycin Assoc w R
gid 4372597 c.669_*34930del frameshift_variant&stop_lost&splice_region_variant 0.91 streptomycin Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.97 streptomycin Uncertain significance 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 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
gyrA 9557 c.2256G>C synonymous_variant 0.95 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 1.0 streptomycin Uncertain significance
Rv1129c 1254327 p.Asp70Asn missense_variant 0.97 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1304610 c.1680C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
PPE35 2164941 c.1290_*2707del frameshift_variant&stop_lost&splice_region_variant 0.91 pyrazinamide Uncertain significance
PPE35 2169099 c.-46955_1513del frameshift_variant&start_lost 0.93 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2725180 c.-1012_*22684del transcript_ablation 0.9 isoniazid Uncertain significance
Rv2680 2991532 c.-4572_*6444del transcript_ablation 0.91 capreomycin Uncertain significance
thyX 3067803 c.-3106_142del frameshift_variant 0.91 para-aminosalicylic_acid
ald 3075157 c.-11662_*4848del transcript_ablation 0.91 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3529550 c.-8021_*38850del transcript_ablation 0.91 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3580551 c.-13883_*31407del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3596281 c.-6701_*15677del transcript_ablation 0.92 pyrazinamide Uncertain significance
Rv3236c 3597595 c.-13955_*14363del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3607969 c.-19196_*3989del transcript_ablation 0.91 pyrazinamide Uncertain significance
Rv3236c 3611044 c.-6658_*914del transcript_ablation 0.9 pyrazinamide Uncertain significance
lpqB 3612933 c.-9843_*10225del transcript_ablation 0.92 bedaquiline
rifampicin Uncertain significance
lpqB 3618841 c.-3809_*4317del transcript_ablation 0.92 bedaquiline
rifampicin Uncertain significance
lpqB 3619810 c.-9154_*3348del transcript_ablation 0.92 bedaquiline
rifampicin Uncertain significance
lpqB 3623041 c.-15340_*117del transcript_ablation 0.91 bedaquiline
rifampicin Uncertain significance
lpqB 3623291 c.1620C>A synonymous_variant 0.94 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624660 p.Ala84Gly missense_variant 0.96 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3831726 c.-9838_*8467del transcript_ablation 0.91 cycloserine
alr 3835012 c.-39663_*5181del transcript_ablation 0.91 cycloserine
alr 3840314 c.-17977_1106del frameshift_variant 0.91 cycloserine
panD 4023963 c.-15142_*19898del transcript_ablation 0.93 pyrazinamide Uncertain significance
glpK 4126422 c.-22887_*11779del transcript_ablation 0.92 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4127803 c.-19439_*10398del transcript_ablation 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4130925 c.-12727_*7276del transcript_ablation 0.92 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4132915 c.-18144_*5286del transcript_ablation 0.92 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4136195 c.-8238_*2006del transcript_ablation 0.94 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.98 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4202552 c.-37310_2973del start_lost&conservative_inframe_deletion 0.93 ethambutol
embA 4236483 c.-6749_*28645del transcript_ablation 0.92 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embA 4242926 c.-306_*36588del transcript_ablation 0.92 ethambutol Uncertain significance
ubiA 4269287 c.-26175_546del start_lost&conservative_inframe_deletion 0.92 ethambutol
ubiA 4269311 p.Trp175Arg missense_variant 0.98 ethambutol Uncertain significance
whiB6 4331441 c.-13873_*6729del transcript_ablation 0.93 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin