TB-Profiler result

Run: ERR117618
Summary

Run ID: ERR117618

Sample name:

Date: 2024-10-05T05:43:03.905131

Number of reads: 5594603

Percentage reads mapped: 99.28

Median coverage: 125.0

Strain: lineage1.1.1

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
lineage1.1 Indo-Oceanic RD239 0.98
lineage1 Indo-Oceanic RD239 0.97
lineage1.1.1 Indo-Oceanic RD239 0.94
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.295delT Assoc w R
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1484G>T Assoc w R
capreomycin rrs n.1484G>T Assoc w R
kanamycin rrs n.1484G>T Assoc w R
cycloserine alr p.Met343Thr Mutation from literature
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
gyrA 7582 p.Asp94Gly missense_variant 0.97 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin Assoc w R
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.92 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.97 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 0.94 isoniazid Assoc w R High-level resistance
pncA 2288946 c.295delT frameshift_variant 0.98 pyrazinamide Assoc w R
alr 3840393 p.Met343Thr missense_variant 0.96 cycloserine Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.97 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
gyrB 6112 p.Met291Ile missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6439 c.1200C>G synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7853 c.552C>T synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8452 p.Ala384Val missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.99 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.99 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.96 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.96 ethionamide
hadA 732110 p.Cys61Gly missense_variant 0.98 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.97 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.99 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.97 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.95 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
rpsL 781821 p.Lys88Glu missense_variant 0.97 streptomycin
rplC 800357 c.-452C>A upstream_gene_variant 0.97 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.98 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.95 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.98 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834184 p.Val215Ile missense_variant 0.96 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.97 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.95 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.94 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.94 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ndh 2101976 p.Pro356Leu missense_variant 0.94 isoniazid Uncertain significance
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.98 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.98 pyrazinamide Uncertain significance
PPE35 2169829 p.Ala262Thr missense_variant 0.97 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223124 p.Leu14Arg missense_variant 0.97 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289517 c.-276C>G upstream_gene_variant 0.93 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.96 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.97 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3074495 c.-24C>T upstream_gene_variant 0.97 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
ald 3087660 c.843dupC frameshift_variant 0.96 cycloserine
Rv3083 3448288 c.-216T>C upstream_gene_variant 0.97 ethionamide
Rv3083 3448714 p.Asp71His missense_variant 0.98 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641951 c.417G>T synonymous_variant 0.95 pretomanid
delamanid
clofazimine
rpoA 3878075 p.Gly145Cys missense_variant 0.36 rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.98 pyrazinamide Not assoc w R - Interim
panD 4044585 c.-304C>T upstream_gene_variant 0.92 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.96 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.96 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.94 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.95 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.96 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.99 ethambutol Not assoc w R
ethA 4326134 p.Pro447Arg missense_variant 0.94 ethionamide
ethA 4326290 p.Ala395Val missense_variant 0.95 ethionamide
ethA 4326398 p.Gln359Arg missense_variant 0.95 ethionamide
whiB6 4338242 p.Gln94Glu missense_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.98 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.97 streptomycin Not assoc w R