TB-Profiler result

Run: SRR1167271
Summary

Run ID: SRR1167271

Sample name:

Date: 2024-10-05T14:17:27.217900

Number of reads: 4534086

Percentage reads mapped: 88.1

Median coverage: 113.0

Strain: lineage4.1.1.3

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 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 0.99
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) 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.-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 embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Arg154Gly Assoc w R
streptomycin rrs n.878G>A Assoc w R - Interim
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine ald c.464delG Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1192_1194dupGTG Mutation from literature
c.869dupA 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 0.94 rifampicin Assoc w R
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.9 streptomycin Assoc w R - Interim
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.66 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 0.99 isoniazid Assoc w R High-level resistance
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide Assoc w R
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.96 ethambutol Assoc w R
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.96 ethionamide Mutation from literature
ethA 4326604 c.869dupA frameshift_variant 1.0 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
gyrB 5184 c.-56_-55insCC upstream_gene_variant 0.12 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 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
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
rpoB 760415 c.609C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.19 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.15 rifampicin
rpoB 762285 p.Arg827Cys missense_variant 0.95 rifampicin Uncertain significance
rpoC 762917 c.-453C>T upstream_gene_variant 0.13 rifampicin
rpoB 762926 c.3120C>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>T synonymous_variant 0.13 rifampicin
rpoC 763573 c.204G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
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
rpsL 781435 c.-125G>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 1.0 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.11 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1473717 n.60G>T non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1473746 n.89T>C non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473811 n.154C>T non_coding_transcript_exon_variant 0.11 capreomycin
linezolid
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473823 n.166T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1473833 n.176G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid
rrl 1475775 n.2118G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.97 capreomycin Not assoc w R
bacA 2063078 c.1650dupG frameshift_variant 0.29 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
katG 2155716 c.394_396delCTTinsTTG synonymous_variant 0.2 isoniazid
katG 2155722 c.390G>C 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A 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
gid 4407798 c.405G>T synonymous_variant 1.0 streptomycin Not assoc w R