TB-Profiler result

Run: SRR21277139
Summary

Run ID: SRR21277139

Sample name:

Date: 2024-04-15T08:03:33.908527

Number of reads: 13043250

Percentage reads mapped: 98.92

Median coverage: 404.0

Strain: lineage2.2.1.1;lineage4.4.2

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
lineage2 East-Asian RD105 0.12
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.11
lineage2.2 East-Asian (Beijing) RD105;RD207 0.11
lineage4 Euro-American None 0.89
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.12
lineage4.4 Euro-American None 0.9
lineage4.4.2 Euro-American None 0.89
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
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461His Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asp461His Assoc w R - Interim
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
gyrB 6620 p.Asp461His missense_variant 0.14 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.12 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.12 streptomycin 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
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
fgd1 491742 c.960T>C synonymous_variant 0.13 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.11 ethionamide Not assoc w R
isoniazid Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800991 c.183G>A synonymous_variant 0.88 linezolid
fbiC 1302692 c.-239C>T upstream_gene_variant 0.11 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
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 2154724 p.Arg463Leu missense_variant 0.12 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.1 pyrazinamide 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
eis 2714846 p.Val163Ile missense_variant 0.11 amikacin Not assoc w R
kanamycin Not assoc w R
folC 2746320 p.Pro427Ala missense_variant 0.88 para-aminosalicylic_acid
Rv2752c 3066099 p.Met31Ile missense_variant 0.9 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.89 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.89 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.13 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.89 ethambutol Not assoc w R
embB 4247249 p.Gly246Arg missense_variant 0.87 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.11 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.89 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.88 ethambutol Not assoc w R
whiB6 4338471 c.51G>A synonymous_variant 0.1 capreomycin Not assoc w R - Interim
amikacin
kanamycin Not assoc w R - Interim
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 0.13 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.15 streptomycin Not assoc w R