TB-Profiler result

Run: ERR11641184
Summary

Run ID: ERR11641184

Sample name:

Date: 2024-04-15T08:38:14.012438

Number of reads: 2472618

Percentage reads mapped: 98.4

Median coverage: 74.0

Strain: lineage4.3.4.2

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.98
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)
p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu120Pro 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 eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ser94Ala Assoc w R - Interim
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 7582 p.Asp94Gly missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674481 p.Ser94Ala missense_variant 0.99 isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim
pncA 2288883 p.Leu120Pro missense_variant 1.0 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.95 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 6817 c.1578G>A synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 8843 p.Glu514Asp missense_variant 0.88 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490949 p.Ser56Cys missense_variant 1.0 clofazimine
pretomanid
delamanid Uncertain significance
rpoB 761408 c.1602G>C synonymous_variant 0.11 rifampicin
rpoB 761477 c.1671C>G synonymous_variant 0.12 rifampicin
rpoB 761492 c.1686G>C synonymous_variant 0.14 rifampicin
rpoB 761510 c.1704T>C synonymous_variant 0.13 rifampicin
rpoC 764995 c.1626C>G synonymous_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.44 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.47 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rpsA 1833424 c.-118C>G upstream_gene_variant 0.11 pyrazinamide
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
katG 2156815 c.-704A>G upstream_gene_variant 1.0 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877962 c.546G>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3878028 c.480G>C synonymous_variant 0.11 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.11 rifampicin
rpoA 3878040 c.468T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3878043 c.465G>A synonymous_variant 0.11 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.11 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.11 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.12 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.16 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878909 c.-402A>G upstream_gene_variant 0.13 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878917 c.-410G>A upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878938 c.-431T>A upstream_gene_variant 0.13 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.11 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4038749 c.1956C>G synonymous_variant 0.18 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.17 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.16 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.2 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.16 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.15 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039004 c.1701C>G synonymous_variant 0.18 pyrazinamide
embC 4239763 c.-100C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248199 c.1686A>G synonymous_variant 0.11 ethambutol
embB 4248208 c.1695C>T synonymous_variant 0.11 ethambutol
embB 4248220 c.1707A>C synonymous_variant 0.13 ethambutol
embB 4248304 c.1791G>C synonymous_variant 0.12 ethambutol
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 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R