TB-Profiler result

Run: SRR29051354
Summary

Run ID: SRR29051354

Sample name:

Date: 2025-02-11T14:51:14.310949

Number of reads: 842168

Percentage reads mapped: 98.57

Median coverage: 24.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: Other

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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 0.93
lineage4.3.4.1 Euro-American (LAM) RD174 0.9
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
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
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.47 streptomycin 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
dnaA 684 c.684G>A synonymous_variant 0.8 isoniazid 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761765 c.1959T>C synonymous_variant 0.2 rifampicin
rpoB 761772 p.His656Ala missense_variant 0.19 rifampicin
rpoB 761778 p.Asn658Asp missense_variant 0.19 rifampicin
rpoB 761858 c.2052G>C synonymous_variant 0.13 rifampicin
rpoB 761873 c.2067A>C synonymous_variant 0.15 rifampicin
rpoB 761885 c.2079T>C synonymous_variant 0.18 rifampicin
rpoB 761906 c.2100C>G synonymous_variant 0.2 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.2 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.18 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.18 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.19 rifampicin
rpoB 761948 c.2142G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.31 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.27 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.26 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.24 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.2 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.21 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 762398 c.-972T>C upstream_gene_variant 0.16 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.16 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.17 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 762419 c.-951C>G upstream_gene_variant 0.16 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.16 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762467 c.-903C>T upstream_gene_variant 0.18 rifampicin
rpoB 762488 c.2682G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762489 p.Val895Gln missense_variant 0.17 rifampicin
rpoB 762857 c.3051C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762860 c.3054G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762863 c.3057T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762971 c.3165G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.16 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.2 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.18 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.18 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.22 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.22 rifampicin
rpoC 764665 c.1296C>G synonymous_variant 0.17 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.94 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 781929 p.Gly124Ser missense_variant 0.14 streptomycin Uncertain significance
sigE 1364434 p.Arg8Trp missense_variant 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.41 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.48 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.33 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rpsA 1833971 c.430C>T synonymous_variant 0.26 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.3 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.29 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.36 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.34 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.28 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.24 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.23 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.98 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154279 c.1833C>T synonymous_variant 0.91 isoniazid Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.95 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.89 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877656 c.852T>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.3 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.3 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.82 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
gid 4408156 p.Leu16Arg missense_variant 0.9 streptomycin Not assoc w R