TB-Profiler result

Run: SRR998825
Summary

Run ID: SRR998825

Sample name:

Date: 2024-04-16T08:56:35.386168

Number of reads: 3509293

Percentage reads mapped: 99.46

Median coverage: 79.0

Strain: lineage4.6.2.2;lineage6.3.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.89
lineage4.6.2 Euro-American RD726 0.83
lineage6.3 West-Africa 2 RD702 0.13
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.86
lineage4 Euro-American None 0.9
lineage6.3.1 West-Africa 2 RD702 0.11
lineage6 West-Africa 2 RD702 0.13
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide pncA p.Ala146Val Assoc w R
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.89 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.85 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
pncA 2288805 p.Ala146Val missense_variant 0.83 pyrazinamide 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 6446 p.Ala403Ser missense_variant 0.13 levofloxacin Not assoc w R
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 9143 c.1842T>C synonymous_variant 0.14 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
gyrA 9591 p.Gly764Arg missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin
Rv0010c 13482 p.Ala26Val missense_variant 0.16 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.14 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.16 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.12 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.17 ethionamide Uncertain significance
nusG 734151 c.-103G>C upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoB 760969 p.Ser388Leu missense_variant 0.12 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.81 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.11 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 0.83 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.14 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.17 ethionamide Uncertain significance
isoniazid Not assoc w R
rpsA 1834564 c.1023C>T synonymous_variant 0.91 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
bacA 2063121 c.1608A>T synonymous_variant 0.14 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
bacA 2063187 c.1542C>T synonymous_variant 0.85 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2102694 p.Val117Ile missense_variant 0.13 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2153986 p.Glu709Ala missense_variant 0.82 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.16 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.16 isoniazid Not assoc w R
katG 2156366 c.-255G>A upstream_gene_variant 0.14 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.14 pyrazinamide Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.16 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746873 p.Met242Ile missense_variant 0.83 para-aminosalicylic_acid
Rv2680 2996208 p.Ala35Asp missense_variant 0.84 capreomycin Uncertain significance
Rv2752c 3064747 p.Gly482Val missense_variant 0.9 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv3083 3448567 p.His22Asp missense_variant 0.93 ethionamide Uncertain significance
Rv3083 3449781 c.1278G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
lpqB 3624350 c.561G>T synonymous_variant 0.15 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877696 p.Thr271Ile missense_variant 0.16 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.14 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138983 p.Val258Gly missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.16 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.83 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.16 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.86 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.17 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.13 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.14 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.81 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.85 ethionamide 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 0.16 streptomycin Not assoc w R