TB-Profiler result

Run: SRR28498699
Summary

Run ID: SRR28498699

Sample name:

Date: 2024-10-04T01:17:56.806719

Number of reads: 1918803

Percentage reads mapped: 99.47

Median coverage: 50.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.19
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.78
lineage4.2.1 Euro-American (TUR) None 0.14
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
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
rpsL 781822 p.Lys88Arg missense_variant 0.18 streptomycin Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.31 kanamycin Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.17 ethambutol Uncertain significance Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.2 ethambutol Uncertain significance Mutation from literature
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 1474 p.Asp492Asn missense_variant 0.25 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491751 c.969C>G synonymous_variant 0.86 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 778924 c.-19G>A upstream_gene_variant 0.79 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779510 c.-605C>T upstream_gene_variant 0.75 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.19 linezolid
fbiC 1303747 p.Thr273Ala missense_variant 0.78 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.76 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.19 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.27 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
ndh 2102887 c.156G>A synonymous_variant 0.85 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714394 p.Glu313Asp missense_variant 0.78 kanamycin Uncertain significance
amikacin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.11 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.13 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.22 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.31 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 0.13 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.22 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.18 kanamycin
capreomycin
amikacin