TB-Profiler result

Run: SRR9971296
Summary

Run ID: SRR9971296

Sample name:

Date: 2025-02-11T11:06:07.807177

Number of reads: 2534304

Percentage reads mapped: 36.78

Median coverage: 73.0

Strain: lineage4.8

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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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
rpoC p.Gly332Arg Uncertain significance Mutation from literature
isoniazid katG p.Asp419His Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.78 rifampicin Uncertain significance Mutation from literature
katG 2154857 p.Asp419His missense_variant 1.0 isoniazid 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 1.0 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.14 rifampicin Uncertain significance
rpoC 766487 p.Pro1040Ser missense_variant 0.23 rifampicin Uncertain significance
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
fbiC 1302983 p.Pro18Leu missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472719 n.874G>A non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.21 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472734 n.889C>A non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472741 n.896G>T non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.31 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 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472805 n.960C>A non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472806 n.961A>T non_coding_transcript_exon_variant 0.18 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472813 n.968A>G non_coding_transcript_exon_variant 0.2 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473128 n.1283C>A non_coding_transcript_exon_variant 0.16 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473134 n.1289T>A non_coding_transcript_exon_variant 0.26 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.33 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 0.31 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473191 n.1346C>G non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473193 n.1348G>T non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473200 n.1355A>C non_coding_transcript_exon_variant 0.3 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.3 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473204 n.1359C>A non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473206 n.1361G>C non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476322 n.2665C>A non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.66 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 1.0 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