TB-Profiler result

Run: SRR17567930
Summary

Run ID: SRR17567930

Sample name:

Date: 2024-10-05T00:58:21.026878

Number of reads: 273342

Percentage reads mapped: 6.82

Median coverage: 7.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 0.99
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.95
lineage4.4 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
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
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
rpoC 762896 c.-474G>C upstream_gene_variant 0.6 rifampicin
rpoB 762917 c.3111C>G synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.67 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.77 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.77 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.69 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.75 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.74 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 764605 c.1236G>C synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.62 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.74 rifampicin
rpoC 764672 p.Gln435Glu missense_variant 0.79 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.73 rifampicin
rpoC 764701 c.1332C>G synonymous_variant 0.68 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Lys missense_variant 0.6 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.78 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.88 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.87 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.89 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.92 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.79 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75 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 0.74 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.74 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.69 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.75 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.77 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 0.76 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 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.76 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 0.74 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.81 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.91 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.94 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.92 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.93 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.91 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476569 n.2912G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476586 n.2929C>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476588 n.2931A>T non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.69 capreomycin
linezolid
rrl 1476602 n.2945G>C non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476607 n.2950C>G non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476611 n.2954T>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476613 n.2956G>C non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476621 n.2964C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476645 n.2988A>G non_coding_transcript_exon_variant 0.65 capreomycin
linezolid
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