TB-Profiler result

Run: ERR163965
Summary

Run ID: ERR163965

Sample name:

Date: 2024-04-15T13:31:34.423536

Number of reads: 2615082

Percentage reads mapped: 92.66

Median coverage: 58.0

Strain: lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.99
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.99
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
isoniazid
ethambutol
pyrazinamide
streptomycin
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
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 6140 p.Val301Leu missense_variant 0.97 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 7760 c.459C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7763 c.462T>C synonymous_variant 0.13 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7799 c.498A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9311 c.2010C>T synonymous_variant 0.13 levofloxacin
moxifloxacin
mshA 575537 p.Asp64Asn missense_variant 0.97 ethionamide Uncertain significance
isoniazid Uncertain significance
nusG 734457 c.204C>G synonymous_variant 0.12 rifampicin
rpoB 760223 c.417T>C synonymous_variant 0.12 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
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
rpsL 781832 c.273T>C synonymous_variant 0.13 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.12 streptomycin
rplC 800648 c.-161A>C upstream_gene_variant 0.13 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.15 linezolid
rplC 801174 c.366T>C synonymous_variant 0.14 linezolid
rplC 801222 c.414T>C synonymous_variant 0.15 linezolid
rplC 801228 c.420T>C synonymous_variant 0.14 linezolid
rplC 801246 c.438C>G synonymous_variant 0.13 linezolid
rplC 801249 c.441T>G synonymous_variant 0.13 linezolid
rplC 801255 c.447C>T synonymous_variant 0.13 linezolid
fbiC 1304034 c.1104A>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834225 c.684C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.15 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783140 p.Thr301Met missense_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyA 3073868 p.Thr202Ala missense_variant 0.94 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
mtrB 3626840 c.-227C>G upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626912 c.438T>C synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3878028 c.480G>C synonymous_variant 0.12 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.13 rifampicin
rpoA 3878040 c.468T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878055 c.453A>G synonymous_variant 0.15 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.13 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.13 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.13 rifampicin
rpoA 3878220 c.288C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3879040 c.-533G>C upstream_gene_variant 0.13 rifampicin
rpoA 3879049 c.-542A>G upstream_gene_variant 0.14 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.95 pyrazinamide Not assoc w R
clpC1 4039586 c.1119G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.21 pyrazinamide
clpC1 4039622 c.1083C>G synonymous_variant 0.19 pyrazinamide
panD 4043938 p.Ile115Thr missense_variant 1.0 pyrazinamide Uncertain significance
glpK 4138571 c.1185C>G synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139575 p.Val61Ile missense_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139581 p.Asn59Asp missense_variant 0.26 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139588 c.168G>C synonymous_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139597 c.157_159delGCCinsAG frameshift_variant&missense_variant 0.23 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139630 c.126C>T synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247389 c.876C>A synonymous_variant 0.11 ethambutol
embB 4248070 c.1557T>C synonymous_variant 0.13 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