TB-Profiler result

Run: ERR4820503
Summary

Run ID: ERR4820503

Sample name:

Date: 2025-09-15T14:47:57.632144

Number of reads: 2176092

Percentage reads mapped: 87.02

Median coverage: 47.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 100.0
lineage2.2 East-Asian (Beijing) RD105;RD207 100.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 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
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
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 762917 c.3111C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763528 c.159G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764470 c.1101C>G synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 764497 c.1128A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.16 rifampicin Uncertain significance
rpoC 764503 c.1134G>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 764507 p.Ala380Ser missense_variant 0.19 rifampicin Uncertain significance
rpoC 764521 c.1152T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.22 rifampicin Uncertain significance
rpoC 764536 c.1167G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.27 rifampicin Uncertain significance
rpoC 764560 c.1191T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.99 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 0.98 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.38 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.45 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.37 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.34 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.34 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472572 n.727T>A non_coding_transcript_exon_variant 0.41 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.43 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.27 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.27 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.32 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.25 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.26 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Uncertain significance
rrs 1472991 n.1146G>A non_coding_transcript_exon_variant 0.3 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.38 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473047 n.1202C>T non_coding_transcript_exon_variant 0.46 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.39 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.4 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.41 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.48 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.42 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.42 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.41 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.38 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.36 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.36 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.33 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.33 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.33 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475871 n.2214T>C non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
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
gid 4407588 c.615A>G synonymous_variant 0.97 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R