TB-Profiler result

Run: SRR14782762
Summary

Run ID: SRR14782762

Sample name:

Date: 2024-03-25T23:38:51.057296

Number of reads: 9799099

Percentage reads mapped: 99.43

Median coverage: 302.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.16
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.85
lineage4.2.1 Euro-American (TUR) None 0.16
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
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
gyrA 7581 p.Asp94Asn missense_variant 0.12 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.15 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.15 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 0.15 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.16 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.15 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 0.16 ethambutol Uncertain significance Mutation from literature
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 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.12 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 0.12 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.17 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.17 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.85 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.15 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
PPE35 2168149 p.Pro822Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.17 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.82 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.13 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
ald 3087220 c.402dupC frameshift_variant 0.11 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.14 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.17 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239930 p.Gly23Glu missense_variant 0.8 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.15 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 0.14 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.16 ethionamide
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 0.16 capreomycin
amikacin
kanamycin