TB-Profiler result

Run: SAMN02381047
Summary

Run ID: SAMN02381047

Sample name:

Date: 2025-09-15T15:31:29.247197

Number of reads: 5216176

Percentage reads mapped: 32.66

Median coverage: 110.0

Strain: 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
lineage4 Euro-American None 100.0
lineage4.6 Euro-American None 100.0
lineage4.6.1 Euro-American (Uganda) RD724 100.0
lineage4.6.1.1 Euro-American RD724 98.3
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 7539 p.Thr80Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
rpoB 762899 c.3093G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 762917 c.3111C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.25 rifampicin Uncertain significance
rpoB 762939 p.Met1045Leu missense_variant 0.26 rifampicin Uncertain significance
rpoB 762942 p.Ile1046Val missense_variant 0.25 rifampicin Uncertain significance
rpoB 762962 c.3156C>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoC 764566 c.1197C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.25 rifampicin Uncertain significance
rpoC 764582 p.Leu405Met missense_variant 0.24 rifampicin Uncertain significance
rpoC 764587 c.1218C>G synonymous_variant 0.29 rifampicin Uncertain significance
rpoC 764605 c.1236G>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764641 c.1272C>T synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764663 p.Val432Thr missense_variant 0.23 rifampicin Uncertain significance
rpoC 764668 c.1299C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764672 p.Gln435Glu missense_variant 0.21 rifampicin Uncertain significance
rpoC 764677 c.1308C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.11 rifampicin Uncertain significance
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 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.39 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.54 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.54 amikacin Uncertain significance
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.5 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.5 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.5 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.44 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.42 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.37 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.25 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.18 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.19 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.32 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.58 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.62 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.59 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.54 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.49 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.33 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.65 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.7 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.68 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.61 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2681 2996876 c.138A>C synonymous_variant 0.99 capreomycin Not assoc w R
whiB7 3569029 c.-350A>G upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Not assoc w R
streptomycin Uncertain significance
glpK 4139297 c.459G>A synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Not assoc w R
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance