TB-Profiler result

Run: SRR1723922
Summary

Run ID: SRR1723922

Sample name:

Date: 2024-10-04T20:54:22.572236

Number of reads: 2133933

Percentage reads mapped: 99.28

Median coverage: 25.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1300_1305delATGGAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1300_1305delATGGAC Mutation from literature
isoniazid katG p.Ser315Ile Assoc w R - Interim High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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 761104 c.1300_1305delATGGAC conservative_inframe_deletion 0.96 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rifampicin Mutation from literature
katG 2155168 p.Ser315Ile missense_variant 0.64 isoniazid Assoc w R - Interim High-level resistance
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 5990 p.Phe251Val missense_variant 1.0 levofloxacin
moxifloxacin
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 7892 c.591G>A synonymous_variant 0.96 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1302973 p.Pro15Ser missense_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1406942 c.396_398delCGC disruptive_inframe_deletion 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834914 p.Lys458Thr missense_variant 0.95 pyrazinamide Uncertain significance
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 2102941 c.102G>A synonymous_variant 0.96 isoniazid Not assoc w R - Interim
delamanid
ethionamide
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2725933 c.-260G>A upstream_gene_variant 1.0 isoniazid
Rv3236c 3613671 c.-555A>G upstream_gene_variant 0.93 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625181 p.Ser478Phe missense_variant 0.95 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrA 3626964 p.Glu129Ala missense_variant 0.96 rifampicin
bedaquiline
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin