TB-Profiler result

Run: ERR1633837
Summary

Run ID: ERR1633837

Sample name:

Date: 2024-04-15T21:14:27.287750

Number of reads: 2490993

Percentage reads mapped: 99.5

Median coverage: 45.0

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.1 Euro-American (X-type) RD183 0.85
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
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 pncA c.-11445_*5256del Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-38290_*8830del Assoc w R
c.-33993_*9028del Assoc w R
c.-28411_*8190del Assoc w R
c.642_*7923del Assoc w R
kanamycin
cycloserine
ethionamide ethA c.-24172_*15700del Assoc w R
c.-25308_*5302del Assoc w R
clofazimine
para-aminosalicylic_acid thyA c.-7007_*21354del Mutation from literature
delamanid fbiD c.-41871_*3056del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.159_*41025del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-15313_*12247del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-13499_*13005del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-7577_*39196del Assoc w R - Interim Confers DLM-PMD cross-resistance
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
tlyA 1879649 c.-38290_*8830del transcript_ablation 0.96 capreomycin Assoc w R
tlyA 1883946 c.-33993_*9028del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1889528 c.-28411_*8190del transcript_ablation 0.97 capreomycin Assoc w R
tlyA 1918580 c.642_*7923del frameshift_variant&stop_lost&splice_region_variant 0.94 capreomycin Assoc w R
pncA 2283424 c.-11445_*5256del transcript_ablation 0.91 pyrazinamide Assoc w R
thyA 3052325 c.-7007_*21354del transcript_ablation 0.95 para-aminosalicylic_acid Mutation from literature
fbiD 3297246 c.-41871_*3056del transcript_ablation 0.96 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3339275 c.159_*41025del frameshift_variant&stop_lost&splice_region_variant 0.91 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3625229 c.-15313_*12247del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3973344 c.-13499_*13005del transcript_ablation 0.95 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3979266 c.-7577_*39196del transcript_ablation 0.94 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ethA 4310303 c.-24172_*15700del transcript_ablation 0.97 ethionamide Assoc w R
ethA 4320701 c.-25308_*5302del transcript_ablation 0.97 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
gyrB 6971 p.Pro578Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 588245 c.-31645_*2001del transcript_ablation 0.93 capreomycin
amikacin
kanamycin
ccsA 604252 c.-15638_*2775del transcript_ablation 0.93 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760196 c.390C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_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
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
Rv1129c 1239373 c.-10547_*13700del transcript_ablation 0.93 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1840204 c.-13401_*35115del transcript_ablation 0.96 linezolid Uncertain significance
tsnR 1853490 c.-116C>G upstream_gene_variant 1.0 linezolid
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 2043739 c.-48_*19069del transcript_ablation 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
PPE35 2164875 c.1240_*2773del stop_lost&conservative_inframe_deletion&splice_region_variant 0.96 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2502190 c.-15924_*20417del transcript_ablation 0.92 isoniazid
ahpC 2726210 c.18T>C synonymous_variant 1.0 isoniazid Not assoc w R - Interim
folC 2734732 c.-20442_*11402del transcript_ablation 0.91 para-aminosalicylic_acid
Rv2477c 2757404 c.-17435_*24961del transcript_ablation 0.95 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2757722 c.-20173_*24643del transcript_ablation 0.96 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ribD 2961588 c.-25250_*625del transcript_ablation 0.96 para-aminosalicylic_acid
Rv2680 2961738 c.-34366_*1795del transcript_ablation 0.97 capreomycin Uncertain significance
Rv2680 2962011 c.-34093_*14451del transcript_ablation 0.94 capreomycin Uncertain significance
Rv2752c 3029569 c.-7756_*34945del transcript_ablation 0.92 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3557295 c.204_*11105del frameshift_variant&stop_lost&splice_region_variant 0.94 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 1.0 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.94 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 0.97 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.97 ethambutol Not assoc w R
aftB 4266519 c.-6531_*433del transcript_ablation 0.97 ethambutol Uncertain significance
whiB6 4335521 c.-24956_*2649del transcript_ablation 0.94 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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