TB-Profiler result

Run: SRR13837960
Summary

Run ID: SRR13837960

Sample name:

Date: 2024-04-15T22:29:33.570759

Number of reads: 1469225

Percentage reads mapped: 99.01

Median coverage: 49.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Pro439Arg Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761122 p.Pro439Arg missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 5192 c.-48C>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 9658 c.2357_2358insT frameshift_variant 1.0 levofloxacin
moxifloxacin
fgd1 490779 c.-4A>T upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
Rv0565c 657379 p.Arg31His missense_variant 1.0 ethionamide
rpoB 760041 p.Gly79Arg missense_variant 1.0 rifampicin
rpoB 760652 c.846C>A synonymous_variant 1.0 rifampicin
mmpL5 775929 p.Asn851Ile missense_variant 1.0 clofazimine
bedaquiline
mmpS5 778941 c.-36A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781149 c.-411C>T upstream_gene_variant 1.0 streptomycin
rpsL 781277 c.-283G>T upstream_gene_variant 1.0 streptomycin
embR 1417376 c.-29T>C upstream_gene_variant 1.0 ethambutol
rrl 1473740 n.83G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1474574 n.917A>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rpsA 1834610 p.Arg357Gly missense_variant 1.0 pyrazinamide
tsnR 1854354 p.Leu250Gln missense_variant 1.0 linezolid
ndh 2101828 c.1215C>T synonymous_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2168706 p.Ser636Phe missense_variant 1.0 pyrazinamide
pncA 2289887 c.-646A>C upstream_gene_variant 1.0 pyrazinamide
folC 2746838 p.Ala254Glu missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2783316 p.Thr243Ala missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987500 p.Gly221Asp missense_variant 1.0 para-aminosalicylic_acid
thyX 3068082 c.-137T>C upstream_gene_variant 1.0 para-aminosalicylic_acid
fbiD 3338954 c.-164A>G upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiD 3339235 p.Leu40Val missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiD 3339406 p.Thr97Ala missense_variant 1.0 clofazimine
pretomanid
delamanid
Rv3083 3448625 p.Leu41Gln missense_variant 1.0 ethionamide
lpqB 3624203 c.708C>T synonymous_variant 1.0 bedaquiline
rifampicin
mtrB 3626461 c.153A>G synonymous_variant 0.98 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626554 c.60A>T synonymous_variant 1.0 bedaquiline
rifampicin
mtrA 3627267 p.Glu28Val missense_variant 1.0 bedaquiline
rifampicin
fbiB 3642247 p.Asn238Thr missense_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3642283 p.Glu250Ala missense_variant 1.0 clofazimine
pretomanid
delamanid
clpC1 4039483 c.1221_1222insC frameshift_variant 1.0 pyrazinamide
glpK 4139747 p.Asp3Glu missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embA 4243843 c.613dupG frameshift_variant 1.0 ethambutol Uncertain significance
embA 4244833 p.Val534Ala missense_variant 1.0 ethambutol
embA 4245735 p.Ala835Ser missense_variant 1.0 ethambutol
aftB 4267994 p.Met281Ile missense_variant 1.0 ethambutol