TB-Profiler result

Run: SRR19303773
Summary

Run ID: SRR19303773

Sample name:

Date: 2024-10-05T09:03:28.032034

Number of reads: 466509

Percentage reads mapped: 15.28

Median coverage: 13.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 1.0
lineage4.6.2 Euro-American RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 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
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
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 1473247 n.1402C>A non_coding_transcript_exon_variant 0.44 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin 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
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
rpoC 764521 c.1152T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.32 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764530 c.1161C>T synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.32 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>G synonymous_variant 0.43 rifampicin
rpoC 764548 c.1179G>C synonymous_variant 0.6 rifampicin
rpoC 764549 p.Pro394Thr missense_variant 0.55 rifampicin
rpoC 764561 p.Pro398Ala missense_variant 0.44 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.62 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.62 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.62 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.69 rifampicin
rpoC 764620 c.1251G>C synonymous_variant 0.38 rifampicin
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.38 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.53 rifampicin Not assoc w R - Interim
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
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.32 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.56 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.42 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.4 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.48 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2155389 c.723C>G synonymous_variant 1.0 isoniazid Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
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