TB-Profiler result

Run: SRR7646056
Summary

Run ID: SRR7646056

Sample name:

Date: 2024-04-16T08:53:59.720391

Number of reads: 1967209

Percentage reads mapped: 23.27

Median coverage: 38.0

Strain: lineage4.2.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 1.0
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 1.0
lineage4.2.1 Euro-American (TUR) 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 gid c.489delA Assoc w R
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
gid 4407713 c.489delA frameshift_variant 1.0 streptomycin Assoc w R
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
Rv0565c 657652 c.-183dupC upstream_gene_variant 0.24 ethionamide
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777451 p.Val344Leu missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 1.0 linezolid
Rv1129c 1254582 c.-48A>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.38 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.7 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.7 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472135 n.290C>G non_coding_transcript_exon_variant 0.71 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.72 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.72 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>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 1472151 n.306C>T non_coding_transcript_exon_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472153 n.308G>C non_coding_transcript_exon_variant 0.76 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.79 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 0.62 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.52 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.51 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.42 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.6 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.86 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 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.88 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.87 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 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472827 n.982G>C non_coding_transcript_exon_variant 0.54 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.49 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.59 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.78 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.79 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.8 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475522 n.1865A>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid Uncertain significance
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475528 n.1871T>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475534 n.1877G>A non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475576 n.1919C>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.87 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.87 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.9 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.89 capreomycin
linezolid
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 1.0 cycloserine
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
rpoA 3877485 c.1023C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408213 c.-11C>T upstream_gene_variant 1.0 streptomycin Uncertain significance