TB-Profiler result

Run: SRR28393820
Summary

Run ID: SRR28393820

Sample name:

Date: 2024-05-22T12:58:10.351290

Number of reads: 4923111

Percentage reads mapped: 99.68

Median coverage: 139.0

Strain: lineage4.1.2.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.68
lineage4.1.2 Euro-American None 0.67
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.69
lineage4.4.1 Euro-American (S-type) None 0.34
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.3
lineage4.4 Euro-American None 0.33
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
p.Leu452Pro Assoc w R
isoniazid katG c.943_945delAGCinsGA Assoc w R High-level resistance
c.18dupA Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
p.Met1000Arg Uncertain significance Mutation from literature
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-15C>G Uncertain significance Mutation from literature
cycloserine
ethionamide ethA c.140delT Assoc w R
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 0.27 rifampicin Assoc w R
rpoB 761161 p.Leu452Pro missense_variant 0.73 rifampicin Assoc w R
katG 2155167 c.943_945delAGCinsGA frameshift_variant&missense_variant 0.67 isoniazid Assoc w R High-level resistance
katG 2156093 c.18dupA frameshift_variant 0.34 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.73 pyrazinamide Assoc w R
eis 2715347 c.-15C>G upstream_gene_variant 0.31 kanamycin Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.69 ethambutol Assoc w R
embB 4249512 p.Met1000Arg missense_variant 0.33 ethambutol Uncertain significance Mutation from literature
ethA 4327333 c.140delT frameshift_variant 0.34 ethionamide 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.63 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.62 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.73 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.68 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.64 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 779414 p.Leu142Arg missense_variant 0.66 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254572 c.-38T>A upstream_gene_variant 0.63 moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
ndh 2102990 p.Val18Ala missense_variant 0.27 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154942 p.Tyr390Trp missense_variant 0.29 isoniazid
PPE35 2169840 p.Gly258Asp missense_variant 0.28 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 2518076 c.-39C>T upstream_gene_variant 0.68 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.15 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.22 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.14 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.34 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.31 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.65 bedaquiline
rifampicin
ddn 3986977 p.Pro45Leu missense_variant 0.27 delamanid Uncertain significance
pretomanid
glpK 4139183 c.572dupG frameshift_variant 0.34 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.33 ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.69 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 0.66 ethambutol Not assoc w R
embC 4243129 c.3267G>A synonymous_variant 0.26 ethambutol Not assoc w R - Interim
embA 4243246 p.Gly5Val missense_variant 0.29 ethambutol Uncertain significance
embB 4245545 c.-969C>T upstream_gene_variant 0.6 ethambutol
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 4407790 p.Ala138Glu missense_variant 0.57 streptomycin Uncertain significance
gid 4407973 p.Val77Ala missense_variant 0.4 streptomycin Uncertain significance