TB-Profiler result

Run: SRR17567930
Summary

Run ID: SRR17567930

Sample name:

Date: 2024-04-14T03:30:19.734256

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 c.3133_3135delATGinsCC frameshift_variant&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 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.89 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.92 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.85 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.69 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.75 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.77 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.81 streptomycin
kanamycin
capreomycin
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 bedaquiline Uncertain significance
rifampicin Not assoc w R