TB-Profiler result

Run: SRR13861221
Summary

Run ID: SRR13861221

Sample name:

Date: 2025-09-15T17:51:55.190616

Number of reads: 4203982

Percentage reads mapped: 70.13

Median coverage: 142.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
dnaA 1209 c.1209C>T synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1230 c.1230A>G synonymous_variant 0.15 isoniazid Uncertain significance
dnaA 1427 p.Ala476Gly missense_variant 0.93 isoniazid Uncertain significance
gyrA 7346 p.Ile15Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8335 p.Met345Arg missense_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9639 p.Gly780Arg missense_variant 0.95 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491505 c.723G>A synonymous_variant 0.96 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 576310 p.Ile321Met missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657451 p.Ala7Val missense_variant 1.0 ethionamide Uncertain significance
mmpL5 775981 p.Leu834Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776732 c.1749C>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777942 p.Pro180Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800343 c.-466G>C upstream_gene_variant 1.0 linezolid Uncertain significance
rplC 800618 c.-191T>C upstream_gene_variant 0.15 linezolid Uncertain significance
fbiC 1303422 c.492A>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1406592 p.Tyr250Cys missense_variant 0.99 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416737 p.Arg204Gln missense_variant 1.0 ethambutol Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475277 n.1620G>C non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834091 p.Val184Met missense_variant 0.93 pyrazinamide Uncertain significance
tlyA 1918473 c.534T>A synonymous_variant 0.98 capreomycin Uncertain significance
Rv1979c 2221849 p.Leu439Gln missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222231 p.Met312Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222710 p.Asn152Ile missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223809 c.-646_-645insT upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
eis 2714723 p.Cys204Gly missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
folC 2746975 p.Asp208Glu missense_variant 0.97 para-aminosalicylic_acid Uncertain significance
Rv2477c 2782420 c.1623T>A synonymous_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783068 p.Asp325Glu 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 2783203 c.840C>T 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 2783221 c.822G>T 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 2783224 c.819C>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 2783719 c.324A>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 2783815 c.228A>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 2783833 c.210G>C 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 2783843 p.Gly67Asp missense_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 2783860 p.Asp61Glu missense_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 2783863 c.180C>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 2783883 c.160T>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 2783884 c.159T>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 2783887 c.156C>G synonymous_variant 0.17 amikacin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
Rv2477c 2783920 c.123G>C synonymous_variant 0.17 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783953 c.90G>A synonymous_variant 0.13 amikacin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Uncertain significance
Rv2477c 2784310 c.-268T>A upstream_gene_variant 0.98 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
pepQ 2860233 c.186T>G synonymous_variant 0.99 bedaquiline Uncertain significance
clofazimine Uncertain significance
thyA 3073781 p.Leu231Ile missense_variant 0.99 para-aminosalicylic_acid Uncertain significance
Rv3083 3448420 c.-84_-83insT upstream_gene_variant 1.0 ethionamide Uncertain significance
whiB7 3568689 c.-11delT upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625750 c.864G>A synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625762 c.852A>G synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625765 c.849C>G synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
mtrB 3625797 p.Val273Met missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.14 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
clpC1 4038748 p.Arg653Cys missense_variant 0.12 pyrazinamide Uncertain significance
clpC1 4039103 c.1602T>C synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039106 c.1599G>C synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039112 c.1593C>G synonymous_variant 0.14 pyrazinamide Uncertain significance
clpC1 4039898 c.807C>G synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039904 c.801A>G synonymous_variant 0.15 pyrazinamide Uncertain significance
clpC1 4039928 c.775_777delAGCinsTCG synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4039931 c.774T>C synonymous_variant 0.17 pyrazinamide Uncertain significance
clpC1 4039946 c.759A>T synonymous_variant 0.19 pyrazinamide Uncertain significance
clpC1 4039952 c.753T>C synonymous_variant 0.18 pyrazinamide Uncertain significance
clpC1 4039958 c.747G>C synonymous_variant 0.18 pyrazinamide Uncertain significance
clpC1 4039979 c.726C>G synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4039996 p.Glu237Gln missense_variant 0.14 pyrazinamide Uncertain significance
clpC1 4040021 c.684A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
embC 4240494 p.Gly211Ala missense_variant 0.98 ethambutol Uncertain significance
embC 4241732 p.Ala624Pro missense_variant 0.95 ethambutol Uncertain significance
embA 4245672 p.Gly814Arg missense_variant 0.94 ethambutol Uncertain significance
embB 4247458 p.Tyr315* stop_gained 0.93 ethambutol Uncertain significance
aftB 4268265 p.Leu191Gln missense_variant 1.0 ethambutol Uncertain significance