TB-Profiler result

Run: SRR13861333
Summary

Run ID: SRR13861333

Sample name:

Date: 2025-09-15T16:16:39.185588

Number of reads: 1408790

Percentage reads mapped: 35.25

Median coverage: 48.0

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 375 p.Asp125Glu missense_variant 1.0 isoniazid Uncertain significance
dnaA 1209 c.1209C>T synonymous_variant 0.14 isoniazid Not assoc w R - Interim
dnaA 1220 p.Asn407Ser missense_variant 0.14 isoniazid Uncertain significance
dnaA 1230 c.1230A>G synonymous_variant 0.14 isoniazid Uncertain significance
gyrB 4996 c.-244A>C upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 5258 p.Lys7* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7122 c.1883_1884insA frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13577 c.-19G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
mmaA3 738206 c.-57G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 762101 c.2295C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.14 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.16 rifampicin Uncertain significance
rpoB 762143 c.2337T>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoB 762995 c.3189G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoB 763085 c.3279C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766483 c.3114G>C synonymous_variant 0.13 rifampicin Uncertain significance
rpoC 766484 p.Val1039Ile missense_variant 0.13 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766495 c.3126C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766522 c.3153C>G synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 766528 c.3159T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766531 c.3162G>T synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766543 c.3174C>T synonymous_variant 0.15 rifampicin Uncertain significance
rpoC 766630 c.3261G>C synonymous_variant 0.15 rifampicin Uncertain significance
mmpL5 776374 p.Arg703Cys missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779126 p.Cys46Phe missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801447 p.Lys213Asn missense_variant 0.98 linezolid Uncertain significance
Rv1129c 1253197 c.1338C>A synonymous_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253317 c.1218G>A synonymous_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253639 p.Leu299* stop_gained 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1303004 p.Ala25Glu missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1303171 p.Arg81Trp missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1303517 p.Met196Thr missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1407597 c.-257C>G upstream_gene_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1833940 c.399C>G synonymous_variant 0.22 pyrazinamide Uncertain significance
rpsA 1833970 c.429G>C synonymous_variant 0.21 pyrazinamide Uncertain significance
rpsA 1833979 c.438T>C synonymous_variant 0.22 pyrazinamide Uncertain significance
rpsA 1834000 c.459G>C synonymous_variant 0.18 pyrazinamide Uncertain significance
rpsA 1834015 c.474G>C synonymous_variant 0.2 pyrazinamide Uncertain significance
rpsA 1834640 p.Glu367* stop_gained 0.93 pyrazinamide Uncertain significance
bacA 2064395 p.Thr112Pro missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
bacA 2064589 c.139delT frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2103004 c.39T>G synonymous_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
PPE35 2170453 p.Gly54Ser missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223326 c.-162C>T upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223365 c.-201C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2288748 p.Ala165Asp missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2518474 p.Glu120Asp missense_variant 0.95 isoniazid Uncertain significance
Rv2477c 2783116 c.927T>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 2783140 c.903C>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
thyX 3067529 c.417C>G synonymous_variant 0.96 para-aminosalicylic_acid Uncertain significance
thyA 3073764 c.708T>C synonymous_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyA 3073862 p.Gly204Ser missense_variant 0.96 para-aminosalicylic_acid Uncertain significance
thyA 3073963 p.Leu170Gln missense_variant 0.94 para-aminosalicylic_acid Uncertain significance
fbiD 3339357 c.240G>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv3083 3448352 c.-152G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
Rv3083 3449624 p.Lys374Met missense_variant 1.0 ethionamide Uncertain significance
Rv3083 3449919 c.1416C>A synonymous_variant 1.0 ethionamide Uncertain significance
fbiB 3642227 p.Gln231His missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiB 3642581 c.1047A>C synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embA 4244641 p.Val470Gly missense_variant 1.0 ethambutol Uncertain significance
embA 4245197 c.1965C>T synonymous_variant 0.95 ethambutol Not assoc w R - Interim
embB 4246641 p.Ala43Glu missense_variant 1.0 ethambutol Uncertain significance
embB 4247233 p.Asp240Glu missense_variant 1.0 ethambutol Uncertain significance
ethA 4327035 p.Tyr147Asp missense_variant 1.0 ethionamide Uncertain significance
ethR 4327923 p.Gln125His missense_variant 1.0 ethionamide Uncertain significance