TB-Profiler result

Run: SRR5341223
Summary

Run ID: SRR5341223

Sample name:

Date: 2024-04-15T20:09:00.948304

Number of reads: 7953132

Percentage reads mapped: 99.31

Median coverage: 232.0

Strain: lineage1.1.2;lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) None 0.14
lineage1.1.2 Indo-Oceanic RD239 0.87
lineage4.2 Euro-American None 0.14
lineage1.1 Indo-Oceanic RD239 0.87
lineage4 Euro-American None 0.13
lineage1 Indo-Oceanic RD239 0.87
lineage4.2.2.2 Euro-American (Ural) None 0.11
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
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Ala504Val 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.Ala504Val Assoc w R - Interim
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
gyrB 6750 p.Ala504Val missense_variant 0.78 moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R - Interim
rpoB 761155 p.Ser450Leu missense_variant 0.14 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.87 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 0.12 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.12 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.11 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 5965 c.726A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6112 p.Met291Ile missense_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.83 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9047 c.1746C>T synonymous_variant 0.83 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.79 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 9328 p.Ala676Val missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9443 c.2142G>A synonymous_variant 0.81 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.82 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.82 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.84 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576000 p.Asp218Ala missense_variant 0.84 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.87 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.87 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.84 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.91 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.12 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.86 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.91 rifampicin Not assoc w R
rpoC 766485 p.Val1039Gly missense_variant 0.12 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 0.81 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.91 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.18 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.87 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.9 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.81 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.85 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.88 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.81 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.84 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 0.82 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.13 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.87 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.85 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.9 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.91 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.9 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.87 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065305 p.Ala296Val missense_variant 0.89 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.13 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.16 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.87 ethionamide Uncertain significance
lpqB 3623459 c.1452G>A synonymous_variant 0.21 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3623909 c.1002C>T synonymous_variant 0.78 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.89 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.82 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
ddn 3987057 p.Arg72Trp missense_variant 0.88 delamanid Uncertain significance
pretomanid
clpC1 4040517 p.Val63Ala missense_variant 0.89 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.89 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.87 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
embC 4240671 p.Thr270Ile missense_variant 0.75 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.92 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 0.82 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.87 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.85 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.89 ethambutol Not assoc w R
whiB6 4338513 c.9C>T synonymous_variant 0.14 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
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 4338603 c.-82C>T upstream_gene_variant 0.88 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 0.8 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.92 streptomycin Not assoc w R