TB-Profiler result

Run: ERR2179802
Summary

Run ID: ERR2179802

Sample name:

Date: 2024-04-15T21:33:26.457845

Number of reads: 3818910

Percentage reads mapped: 93.25

Median coverage: 102.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 0.82
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 gid c.-1891_*16123del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA c.-34695_*9469del Assoc w R
c.-14191_*27235del Assoc w R
c.-13814_*14175del Assoc w R
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyA c.-3673_*21621del Mutation from literature
c.-15519_*253del Mutation from literature
delamanid fbiC c.-5398_*4622del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD c.-21343_*21671del Assoc w R - Interim Confers DLM-PMD cross-resistance
c.-8641_*32906del Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA c.-11212_*25330del Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn c.-16525_*10640del 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
fbiC 1297532 c.-5398_*4622del transcript_ablation 0.91 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
tlyA 1883244 c.-34695_*9469del transcript_ablation 0.92 capreomycin Assoc w R
tlyA 1903748 c.-14191_*27235del transcript_ablation 0.94 capreomycin Assoc w R
tlyA 1904125 c.-13814_*14175del transcript_ablation 0.93 capreomycin Assoc w R
thyA 3052058 c.-3673_*21621del transcript_ablation 0.91 para-aminosalicylic_acid Mutation from literature
thyA 3073426 c.-15519_*253del transcript_ablation 0.95 para-aminosalicylic_acid Mutation from literature
fbiD 3317774 c.-21343_*21671del transcript_ablation 0.92 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiD 3330476 c.-8641_*32906del transcript_ablation 0.94 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
fbiA 3629330 c.-11212_*25330del transcript_ablation 0.95 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
ddn 3970318 c.-16525_*10640del transcript_ablation 0.95 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
gid 4391404 c.-1891_*16123del transcript_ablation 0.91 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 7892 c.591G>A synonymous_variant 1.0 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
ccsA 620029 c.139C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
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 801071 p.Asp88Ala missense_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1820964 c.-12577_*3996del transcript_ablation 0.92 pyrazinamide Uncertain significance
tsnR 1842190 c.-11415_*19410del transcript_ablation 0.9 linezolid Uncertain significance
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 2045975 c.-23467_*16833del transcript_ablation 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
ndh 2103140 c.-98G>A upstream_gene_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2166655 c.1242_*993del frameshift_variant&stop_lost&splice_region_variant 0.92 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 1.0 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
kasA 2475628 c.-42486_518del frameshift_variant 0.92 isoniazid
kasA 2514783 c.-3331_*20048del transcript_ablation 0.91 isoniazid
folC 2746469 c.-33165_1129del frameshift_variant&start_lost 0.94 para-aminosalicylic_acid
Rv2477c 2764065 c.-15043_*18300del 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 2784217 c.-211_-176delATCTCCCGGCCGCCACGGGGACCGGGGCGGCCGGTG upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2966645 c.-29459_*5940del transcript_ablation 0.94 capreomycin Uncertain significance
Rv3083 3444364 c.-4139_*7441del transcript_ablation 0.93 ethionamide Uncertain significance
whiB7 3567522 c.-31809_*878del transcript_ablation 0.93 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3600772 c.-15773_*11186del transcript_ablation 0.93 pyrazinamide Uncertain significance
Rv3236c 3604228 c.-28272_*7730del transcript_ablation 0.95 pyrazinamide Uncertain significance
Rv3236c 3610290 c.-18426_*1668del transcript_ablation 0.92 pyrazinamide Uncertain significance
Rv3236c 3611509 c.-5065_*449del transcript_ablation 0.95 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641684 c.150C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3841257 c.-26648_163del frameshift_variant 0.92 cycloserine
rpoA 3848299 c.-3686_*29164del transcript_ablation 0.94 rifampicin
rpoA 3868357 c.-18010_*9106del transcript_ablation 0.91 rifampicin
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
panD 4011760 c.-5107_*32101del transcript_ablation 0.94 pyrazinamide Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
glpK 4138661 c.-5086_1094del frameshift_variant 0.93 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4219144 c.-20718_*2497del transcript_ablation 0.94 ethambutol
embA 4221939 c.-21293_*21656del transcript_ablation 0.96 ethambutol Uncertain significance
embC 4222228 c.-17634_2952del start_lost&conservative_inframe_deletion 0.92 ethambutol
embA 4240512 c.-2720_*530del transcript_ablation 0.95 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4244276 c.-2237_663del start_lost&conservative_inframe_deletion 0.97 ethambutol
aftB 4256570 c.-28709_*10382del transcript_ablation 0.94 ethambutol 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