TB-Profiler result

Run: SRR1173832
Summary

Run ID: SRR1173832

Sample name:

Date: 2025-02-11T19:23:37.939782

Number of reads: 738172

Percentage reads mapped: 39.63

Median coverage: 15.0

Strain: lineage3.1;lineage4.6.1.1

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.62
lineage4.6 Euro-American None 0.25
lineage4.6.1.1 Euro-American RD724 0.21
lineage4.6.1 Euro-American (Uganda) RD724 0.21
lineage3.1 East-African-Indian RD750 0.6
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
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
fgd1 491742 c.960T>C synonymous_variant 0.68 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.62 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.79 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.75 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.22 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.31 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.49 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.41 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.71 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 0.62 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 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.2 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 0.2 capreomycin Uncertain significance
linezolid
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.21 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 0.2 capreomycin
linezolid
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.72 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.77 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.58 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.71 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.62 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.51 capreomycin Not assoc w R
linezolid Uncertain significance
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
katG 2154724 p.Arg463Leu missense_variant 0.45 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.76 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
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82 isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.74 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.73 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.81 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.56 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.67 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407742 p.Arg154Gln missense_variant 0.39 streptomycin