TB-Profiler result

Run: SRR29231786
Summary

Run ID: SRR29231786

Sample name:

Date: 2024-10-03T17:14:34.449435

Number of reads: 3628222

Percentage reads mapped: 99.57

Median coverage: 111.0

Strain: lineage4.1.1.1;lineage4.1.2;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.33
lineage4.1 Euro-American None 0.7
lineage4.1.1.1 Euro-American (X-type) RD183 0.45
lineage4.1.2 Euro-American None 0.22
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.47
lineage4.3.3 Euro-American (LAM) RD115 0.31
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
rpoB 761161 p.Leu452Pro missense_variant 0.32 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.28 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.33 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
dnaA 698 p.Arg233Pro missense_variant 0.27 isoniazid Uncertain significance
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 0.3 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
fgd1 491616 p.Glu278Asp missense_variant 0.35 pretomanid
delamanid
clofazimine
Rv0565c 657269 p.Ser68Pro missense_variant 0.59 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.26 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.65 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776417 c.2064G>A synonymous_variant 0.22 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781676 c.117C>T synonymous_variant 0.32 streptomycin Not assoc w R - Interim
rplC 800219 c.-590T>C upstream_gene_variant 0.48 linezolid
Rv1129c 1254179 p.Ser119Asn missense_variant 0.34 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
sigE 1364205 c.-208G>C upstream_gene_variant 0.43 pyrazinamide
embR 1417140 p.Ala70Ser missense_variant 0.29 ethambutol Not assoc w R
embR 1418018 c.-671C>T upstream_gene_variant 0.28 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476055 n.2398C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
inhA 1673249 c.-953C>T upstream_gene_variant 0.28 isoniazid
ethionamide
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.27 isoniazid
ahpC 2726210 c.18T>C synonymous_variant 0.46 isoniazid Not assoc w R - Interim
folC 2747022 p.Val193Ile missense_variant 0.12 para-aminosalicylic_acid
folC 2747044 c.555C>T synonymous_variant 0.13 para-aminosalicylic_acid
Rv2680 2996519 p.Val139Met missense_variant 0.34 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.33 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339550 p.Gly145Arg missense_variant 0.47 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3083 3448894 p.Tyr131Asp missense_variant 0.22 ethionamide Uncertain significance
Rv3083 3449642 p.Asn380Ser missense_variant 0.33 ethionamide Uncertain significance
whiB7 3568921 c.-242G>C upstream_gene_variant 0.21 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.23 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 0.57 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
rpoA 3877553 p.Glu319Lys missense_variant 0.5 rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.35 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.23 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240897 c.1035C>G synonymous_variant 0.47 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.73 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.51 ethambutol Not assoc w R
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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.28 streptomycin Not assoc w R