TB-Profiler result

Run: SRR13861564
Summary

Run ID: SRR13861564

Sample name:

Date: 2024-10-04T00:30:35.629184

Number of reads: 1416130

Percentage reads mapped: 35.44

Median coverage: 47.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
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 1204 c.1204C>T synonymous_variant 0.13 isoniazid
gyrB 6715 c.1476C>T synonymous_variant 0.98 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 8636 c.1335A>G synonymous_variant 0.13 levofloxacin
moxifloxacin
fgd1 491217 c.435T>C synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491232 c.450T>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fgd1 491241 p.Asp153Glu missense_variant 0.15 pretomanid
delamanid
clofazimine
fgd1 491244 c.462T>C synonymous_variant 0.17 pretomanid
delamanid
clofazimine
mshA 575693 p.Pro116Ala missense_variant 0.96 isoniazid
ethionamide
nusG 734493 p.Phe80Leu missense_variant 0.91 rifampicin
rpoB 759863 p.Gln19His missense_variant 1.0 rifampicin
rpoB 760399 p.Val198Ala missense_variant 0.93 rifampicin
rpoB 763150 p.Phe1115Tyr missense_variant 0.9 rifampicin
rpoC 764516 p.Asp383Asn missense_variant 0.9 rifampicin
rpoC 766103 p.Arg912Gly missense_variant 0.95 rifampicin
mmpL5 777066 p.Ile472Ser missense_variant 1.0 bedaquiline
clofazimine
rpsL 781333 c.-227C>G upstream_gene_variant 1.0 streptomycin
rplC 800612 c.-197A>G upstream_gene_variant 0.14 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.16 linezolid
rplC 800648 c.-161A>C upstream_gene_variant 0.14 linezolid
embR 1417750 c.-403G>C upstream_gene_variant 1.0 ethambutol
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.54 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.57 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.53 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.51 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674507 c.306G>C synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674537 c.336C>G synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.14 isoniazid
ethionamide
inhA 1674549 c.348G>C synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674555 c.354G>A synonymous_variant 0.14 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
inhA 1674564 c.363C>T synonymous_variant 0.14 isoniazid Not assoc w R - Interim
ethionamide
inhA 1674582 c.381T>C synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.17 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.18 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674627 c.426T>G synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674630 c.429C>G synonymous_variant 0.2 isoniazid
ethionamide
inhA 1674636 c.435C>G synonymous_variant 0.2 isoniazid
ethionamide
bacA 2063818 c.910delC frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
ndh 2103185 c.-143A>C upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
PPE35 2168894 c.1718dupG frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170039 p.Ala192Thr missense_variant 1.0 pyrazinamide
Rv1979c 2221777 p.Ala463Val missense_variant 1.0 bedaquiline
clofazimine
kasA 2518793 p.Ser227Thr missense_variant 0.94 isoniazid
ahpC 2726300 c.108C>A synonymous_variant 0.96 isoniazid
folC 2747094 p.Asp169His missense_variant 1.0 para-aminosalicylic_acid
Rv2752c 3064936 p.Ser419* stop_gained 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065523 c.669C>T synonymous_variant 0.98 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
Rv2752c 3066039 c.153C>T synonymous_variant 0.91 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
lpqB 3623677 p.Val412Phe missense_variant 1.0 rifampicin
bedaquiline
alr 3841286 c.135T>A synonymous_variant 1.0 cycloserine
clpC1 4039268 c.1437C>G synonymous_variant 0.12 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039289 c.1416T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039295 c.1410A>C synonymous_variant 0.13 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039368 p.Lys446Thr missense_variant 0.91 pyrazinamide
clpC1 4039553 c.1152C>G synonymous_variant 0.12 pyrazinamide
embC 4241777 p.Gly639Ser missense_variant 1.0 ethambutol
ubiA 4269888 c.-55C>A upstream_gene_variant 1.0 ethambutol