TB-Profiler result

Run: SRR11972381
Summary

Run ID: SRR11972381

Sample name:

Date: 2024-10-05T10:16:09.880693

Number of reads: 837275

Percentage reads mapped: 99.42

Median coverage: 23.0

Strain: lineage1.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.24
lineage1.1 Indo-Oceanic RD239 0.23
lineage1 Indo-Oceanic RD239 0.35
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 371 p.Pro124Leu missense_variant 0.69 isoniazid Not assoc w R
gyrB 5436 p.Asn66Ser missense_variant 0.41 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6084 p.Gly282Val missense_variant 0.33 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.53 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.44 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.35 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.43 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657099 c.372C>T synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.27 ethionamide
mmaA3 738018 c.132C>T synonymous_variant 0.33 isoniazid
rpoB 763031 c.3225T>C synonymous_variant 0.46 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.35 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.33 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.5 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.48 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.31 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406150 c.1191G>A synonymous_variant 0.8 streptomycin
pyrazinamide
isoniazid
embR 1417554 c.-207C>G upstream_gene_variant 0.32 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.25 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1853974 c.369C>T synonymous_variant 0.57 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.62 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.38 linezolid Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.29 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102547 p.Arg166Trp missense_variant 0.41 isoniazid
delamanid
ethionamide
PPE35 2167926 p.Leu896Ser missense_variant 0.24 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.3 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.48 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 0.42 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23 isoniazid
Rv2680 2995823 c.-282_-281insCGT upstream_gene_variant 0.64 capreomycin
Rv2752c 3064632 c.1560C>T synonymous_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3065540 p.Val218Leu missense_variant 0.57 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.33 cycloserine
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.9 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.46 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840764 c.657G>C synonymous_variant 0.67 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.61 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.29 ethambutol Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.24 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.41 kanamycin
capreomycin
amikacin