TB-Profiler result

Run: SAMN02360562
Summary

Run ID: SAMN02360562

Sample name:

Date: 2024-10-04T16:43:27.068246

Number of reads: 6284960

Percentage reads mapped: 37.14

Median coverage: 140.0

Strain: lineage4.4.2

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 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
lineage4.4.2 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 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.Ser140Asn Uncertain significance Mutation from literature
ahpC c.-48G>A Uncertain significance Mutation from literature
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA p.Thr100Pro Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin gyrB p.Ala504Thr Uncertain significance Mutation from literature
gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Ala504Thr Uncertain significance Mutation from literature
gyrA p.Asp94Ala Assoc w R
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
gyrB 6749 p.Ala504Thr missense_variant 1.0 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Ala missense_variant 1.0 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
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)
katG 2155693 p.Ser140Asn missense_variant 0.28 isoniazid Uncertain significance Mutation from literature
pncA 2288944 p.Thr100Pro missense_variant 1.0 pyrazinamide Assoc w R - Interim
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala 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
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
rpoB 759939 p.Pro45Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 762893 c.-477C>T upstream_gene_variant 0.14 rifampicin
rpoC 762896 c.-474G>C upstream_gene_variant 0.14 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.18 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.18 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.18 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.18 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.16 rifampicin
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
Rv1129c 1254565 c.-31T>C upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471832 n.-14A>G upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.17 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.11 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.3 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833692 p.Val51Leu missense_variant 0.99 pyrazinamide
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
katG 2154134 p.Asn660Asp missense_variant 0.99 isoniazid Uncertain significance
katG 2155613 p.Phe167Leu missense_variant 0.14 isoniazid
katG 2155614 c.498T>C synonymous_variant 0.14 isoniazid
katG 2155617 p.Ile165Met missense_variant 0.15 isoniazid
katG 2155626 c.486G>C synonymous_variant 0.21 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.19 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.19 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.2 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.21 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.25 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.28 isoniazid
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.28 isoniazid Not assoc w R - Interim
katG 2155704 c.408C>T synonymous_variant 0.28 isoniazid
katG 2155716 c.396T>C synonymous_variant 0.27 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.23 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.22 isoniazid
katG 2155735 p.Met126Gln missense_variant 0.21 isoniazid
katG 2155737 c.375C>T synonymous_variant 0.22 isoniazid
katG 2155741 p.Gly124Ala missense_variant 0.22 isoniazid Uncertain significance
katG 2155743 c.369G>T synonymous_variant 0.21 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pepQ 2860227 c.192C>G synonymous_variant 0.99 bedaquiline
clofazimine
Rv2752c 3066099 p.Met31Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
thyX 3067949 c.-4C>T upstream_gene_variant 0.95 para-aminosalicylic_acid
thyA 3074057 p.Glu139* stop_gained 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087182 c.364_532del frameshift_variant 0.99 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841392 p.Lys10Met missense_variant 1.0 cycloserine
rpoA 3878157 c.351C>G synonymous_variant 1.0 rifampicin
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embA 4242472 c.-761G>C upstream_gene_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267262 c.1575T>C synonymous_variant 1.0 ethambutol
ubiA 4268928 c.906C>T synonymous_variant 0.99 ethambutol Not assoc w R
ubiA 4269296 p.Met180Val missense_variant 0.99 ethambutol Uncertain significance
ubiA 4269375 c.459G>A synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326860 p.Leu205Pro missense_variant 1.0 ethionamide Uncertain significance
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
gid 4408103 p.Gly34Trp missense_variant 0.91 streptomycin Uncertain significance