TB-Profiler result

Run: ERR4797089
Summary

Run ID: ERR4797089

Sample name:

Date: 2024-03-26T16:01:14.661458

Number of reads: 5907984

Percentage reads mapped: 99.52

Median coverage: 149.0

Strain: lineage1.1.3.1;lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 0.31
lineage1.1.3 Indo-Oceanic RD239 0.68
lineage1.1 Indo-Oceanic RD239 0.64
lineage4 Euro-American None 0.3
lineage1 Indo-Oceanic RD239 0.65
lineage1.1.3.1 Indo-Oceanic RD239 0.66
lineage4.3.3 Euro-American (LAM) RD115 0.33
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 pncA p.Ala171Val Uncertain significance Mutation from literature
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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.223_226dupATCG 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
gyrA 7570 p.Ala90Val missense_variant 0.35 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid Assoc w R High-level resistance
pncA 2288730 p.Ala171Val missense_variant 0.45 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.36 ethambutol Assoc w R
ethA 4327247 c.223_226dupATCG frameshift_variant 0.18 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
dnaA 1044 p.Met348Ile missense_variant 0.34 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.67 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8040 p.Gly247Ser missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.63 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.69 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9276 p.Leu659Val missense_variant 0.72 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.79 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.57 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.66 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.65 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.74 rifampicin Not assoc w R
nusG 734264 p.Phe4Ser missense_variant 0.61 rifampicin Uncertain significance
rpoB 762929 c.3123G>A synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.68 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.54 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.56 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Thr missense_variant 0.4 rifampicin Uncertain significance
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 0.76 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
rplC 800357 c.-452C>A upstream_gene_variant 0.71 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.73 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.67 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.7 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.63 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474301 n.644G>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rpsA 1834836 p.Met432Thr missense_variant 0.37 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.64 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.63 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
bacA 2062922 p.Ile603Val missense_variant 0.64 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2153940 c.2172C>T synonymous_variant 0.77 isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.68 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.32 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.74 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.76 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.8 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 2289351 c.-110C>A upstream_gene_variant 0.63 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.72 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.35 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.71 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.37 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.73 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.34 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.73 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.77 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841253 c.168C>T synonymous_variant 0.65 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.26 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.63 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139183 c.573T>G synonymous_variant 0.3 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240671 p.Thr270Ile missense_variant 0.5 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.59 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.56 ethambutol Not assoc w R
embA 4244099 c.867T>C synonymous_variant 0.62 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.64 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.78 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.74 ethambutol Not assoc w R
ubiA 4269391 p.Val148Ala missense_variant 0.27 ethambutol Uncertain significance
ubiA 4269606 c.228T>C synonymous_variant 0.73 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.76 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.8 streptomycin Not assoc w R - Interim
gid 4407806 p.Ala133Thr missense_variant 0.27 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.64 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.31 streptomycin Not assoc w R