TB-Profiler result

Run: ERR1035315
Summary

Run ID: ERR1035315

Sample name:

Date: 2024-04-15T20:45:28.951491

Number of reads: 6245207

Percentage reads mapped: 98.43

Median coverage: 70.0

Strain: lineage4.3.4.1

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
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.4.1 Euro-American (LAM) RD174 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 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 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)
p.Ile194Thr Uncertain significance Mutation from literature
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Asp63His Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
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 7582 p.Asp94Gly missense_variant 1.0 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
pncA 2289055 p.Asp63His missense_variant 1.0 pyrazinamide Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.97 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol 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 6028 c.789C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 8639 c.1338G>A synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759608 c.-199C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 759940 p.Pro45Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.98 rifampicin Not assoc w R
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 0.98 streptomycin Not assoc w R
rplC 801066 c.258G>A synonymous_variant 1.0 linezolid Not assoc w R - Interim
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.42 capreomycin
linezolid Uncertain significance
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid Uncertain significance
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.21 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.33 capreomycin
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.98 capreomycin 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
ahpC 2726323 p.Pro44Arg missense_variant 1.0 isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.96 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448598 p.Ile32Thr missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878270 p.Leu80Val missense_variant 0.98 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4268982 c.852G>A synonymous_variant 1.0 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R