TB-Profiler result

Run: SRR13861326
Summary

Run ID: SRR13861326

Sample name:

Date: 2025-09-15T16:23:24.986342

Number of reads: 2297538

Percentage reads mapped: 57.49

Median coverage: 77.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.Arg460Cys Mutation from literature
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
embB 4247891 p.Arg460Cys missense_variant 0.93 ethambutol Mutation from literature
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
gyrB 6088 c.849C>A synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
hadA 731690 c.-240A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
hadA 732094 c.165T>C synonymous_variant 1.0 isoniazid Uncertain significance
nusG 734764 p.Ala171Ser missense_variant 0.97 rifampicin Uncertain significance
rpoB 760181 c.375T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760328 c.522G>C synonymous_variant 0.13 rifampicin Uncertain significance
rpoB 760730 c.924T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761786 c.1980C>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 763945 c.576T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 763960 c.591T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763967 p.Gly200Ser missense_variant 0.13 rifampicin Uncertain significance
rpoC 764040 p.Ser224Asn missense_variant 0.13 rifampicin Uncertain significance
rpoC 764626 c.1257C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764973 p.Asp535Ala missense_variant 0.93 rifampicin Uncertain significance
rpoC 766390 c.3021C>T synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766408 c.3039C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766447 c.3078T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766483 c.3114G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766484 p.Val1039Ile missense_variant 0.14 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766495 c.3126C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766522 c.3153C>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 766528 c.3159T>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766531 c.3162G>T synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766543 c.3174C>T synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766549 c.3180G>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766573 c.3204T>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766583 p.Gly1072Ser missense_variant 0.19 rifampicin Uncertain significance
rpoC 766588 c.3219G>A synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766591 c.3222A>G synonymous_variant 0.19 rifampicin Uncertain significance
rpoC 766594 c.3225G>C synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 766607 p.Ile1080Leu missense_variant 0.17 rifampicin Uncertain significance
rpoC 766630 c.3261G>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766645 c.3276A>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 766651 c.3282T>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766657 c.3288A>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 766672 c.3303T>C synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766738 c.3369G>T synonymous_variant 0.12 rifampicin Uncertain significance
rpoC 766750 c.3381C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766933 c.3564A>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766945 c.3576A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767009 p.Ser1214Thr missense_variant 0.14 rifampicin Uncertain significance
rpoC 767014 c.3645G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 767059 c.3690T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin Uncertain significance
rpoC 767074 c.3705T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 767098 c.3729T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 767158 c.3789T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767167 c.3798C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.15 rifampicin Uncertain significance
rpoC 767191 c.3822C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpsL 781532 c.-28G>T upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800224 c.-585G>C upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1302843 c.-88A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1302887 c.-43delG upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrl 1473434 n.-224T>C upstream_gene_variant 0.97 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473813 n.156C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>A non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833260 c.-282G>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
rpsA 1833724 c.183C>G synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1833727 c.186G>C synonymous_variant 0.16 pyrazinamide Uncertain significance
rpsA 1833742 c.201A>G synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1833787 c.246C>G synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1833790 c.249T>A synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1833799 c.258C>G synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834396 c.855G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834411 c.870T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
rpsA 1834435 c.894G>C synonymous_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834498 c.957C>T synonymous_variant 0.13 pyrazinamide Uncertain significance
katG 2156364 c.-253T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2221814 p.Leu451Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222030 p.Val379Met missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2518687 c.573C>T synonymous_variant 0.13 isoniazid Uncertain significance
kasA 2518696 c.582C>G synonymous_variant 0.13 isoniazid Uncertain significance
kasA 2518717 c.603C>T synonymous_variant 0.15 isoniazid Uncertain significance
kasA 2518723 p.Glu203Asp missense_variant 0.14 isoniazid Uncertain significance
kasA 2518732 c.618C>G synonymous_variant 0.15 isoniazid Uncertain significance
kasA 2519238 p.Thr375Lys missense_variant 1.0 isoniazid Uncertain significance
folC 2747285 p.Val105Ala missense_variant 0.97 para-aminosalicylic_acid Uncertain significance
Rv2477c 2783110 c.933C>A synonymous_variant 0.13 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783116 c.927T>C synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783203 c.840C>T synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783221 c.822G>T synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783243 p.Thr267Ser missense_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783247 c.796T>C synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783254 c.789A>G synonymous_variant 0.15 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783263 c.780G>C synonymous_variant 0.16 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783278 c.765A>G synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783287 c.756C>G synonymous_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783290 c.753G>C synonymous_variant 0.13 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783578 p.Glu155Asp missense_variant 0.13 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2784556 c.-514A>C upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
pepQ 2859712 p.Thr236Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2681 2996593 c.-146T>C upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv2681 2997178 p.Val147Glu missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065064 c.1128G>T synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyX 3068085 c.-140T>A upstream_gene_variant 0.99 para-aminosalicylic_acid Uncertain significance
ald 3087003 p.Asp62His missense_variant 1.0 cycloserine Uncertain significance
Rv3083 3448914 p.Ile137Met missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568676 p.Ser2Pro missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625172 p.Thr481Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3625687 c.-777G>C upstream_gene_variant 0.13 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3625696 c.-786A>G upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625705 c.909C>G synonymous_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
lpqB 3625714 c.-804C>T upstream_gene_variant 0.17 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625720 c.894G>C synonymous_variant 0.18 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625729 c.885A>G synonymous_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625735 c.879C>A synonymous_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625750 c.864G>A synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625797 p.Val273Met missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3641491 p.Ala317Pro missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3840235 p.Gly372* stop_gained 0.99 cycloserine Uncertain significance
alr 3840304 c.1044delT frameshift_variant 0.94 cycloserine Uncertain significance
alr 3841263 p.Arg29His missense_variant 1.0 cycloserine Uncertain significance
rpoA 3878082 c.426T>C synonymous_variant 0.13 rifampicin Uncertain significance
glpK 4139790 c.-35C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.12 ethambutol Not assoc w R
embC 4240706 p.Val282Thr missense_variant 0.13 ethambutol Uncertain significance
embC 4240726 c.864G>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embC 4240789 c.927T>C synonymous_variant 0.14 ethambutol Uncertain significance
embC 4241029 p.Trp389* stop_gained 0.95 ethambutol Uncertain significance
embB 4249631 p.Thr1040Pro missense_variant 0.98 ethambutol Uncertain significance
ethA 4327197 p.Gly93Arg missense_variant 1.0 ethionamide Uncertain significance