TB-Profiler result

Run: SRR28044892
Summary

Run ID: SRR28044892

Sample name:

Date: 2024-05-22T15:28:11.517528

Number of reads: 9769048

Percentage reads mapped: 99.5

Median coverage: 243.0

Strain: lineage1.1.2;lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.12
lineage4.1 Euro-American None 0.81
lineage1.1 Indo-Oceanic RD239 0.14
lineage4.1.1.3 Euro-American (X-type) RD193 0.86
lineage4 Euro-American None 0.83
lineage4.1.1 Euro-American (X-type) None 0.84
lineage1 Indo-Oceanic RD239 0.14
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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 p.Leu35Pro Assoc w R - Interim
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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 0.79 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.82 isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid Assoc w R High-level resistance
pncA 2289138 p.Leu35Pro missense_variant 0.76 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.91 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.86 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 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.16 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.12 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.86 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.16 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.17 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.83 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.18 rifampicin Not assoc w R
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 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.83 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.14 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.19 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 0.15 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.18 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474177 n.520T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.16 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 0.12 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.17 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.18 pyrazinamide Uncertain significance
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 0.15 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.13 isoniazid
ribD 2987612 c.774C>T synonymous_variant 0.17 para-aminosalicylic_acid
Rv2681 2996912 c.174C>T synonymous_variant 0.23 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.19 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.23 ethionamide Uncertain significance
Rv3236c 3612263 p.Gly285Glu missense_variant 0.15 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.16 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 0.15 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
rpoA 3879106 c.-599G>A upstream_gene_variant 0.18 rifampicin
clpC1 4040517 p.Val63Ala missense_variant 0.24 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.22 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 4241042 p.Asn394Asp missense_variant 0.13 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 0.82 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.15 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.18 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.27 ethambutol
embB 4247033 p.Ser174Arg missense_variant 0.16 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.23 ethambutol Not assoc w R
embB 4247905 c.1392G>C synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embB 4249100 p.Tyr863His missense_variant 0.1 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.86 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.2 ethambutol Not assoc w R
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 0.2 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.14 streptomycin Not assoc w R