TB-Profiler result

Run: ERR7902673
Summary

Run ID: ERR7902673

Sample name:

Date: 2024-04-15T02:19:51.301178

Number of reads: 3371938

Percentage reads mapped: 99.27

Median coverage: 109.0

Strain: lineage1.1.2;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.85
lineage4.1 Euro-American None 0.14
lineage4.1.2 Euro-American None 0.14
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.12
lineage1.1 Indo-Oceanic RD239 0.88
lineage4 Euro-American None 0.14
lineage1 Indo-Oceanic RD239 0.84
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ser104Ile Assoc w R - Interim
streptomycin rrs n.514A>C Assoc w R
gid c.468_475delCGGGCGAA Assoc w R
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 761155 p.Ser450Leu missense_variant 0.85 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.92 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288931 p.Ser104Ile missense_variant 0.86 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.85 ethambutol Assoc w R
gid 4407727 c.468_475delCGGGCGAA frameshift_variant 0.89 streptomycin Assoc w R
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 6112 p.Met291Ile missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.83 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.89 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.83 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.15 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.82 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.13 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.1 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.87 ethionamide
hadA 732154 c.225G>C synonymous_variant 0.85 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.85 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.15 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.92 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.83 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.87 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.85 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpR5 778079 c.-911C>T upstream_gene_variant 0.17 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800250 c.-559C>G upstream_gene_variant 0.89 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.86 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.86 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.85 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.85 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.85 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674572 p.Ala124Val missense_variant 0.42 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.85 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.83 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.86 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.88 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.9 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.93 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.17 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.85 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.85 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.83 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339741 c.624G>A synonymous_variant 0.86 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.87 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.84 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.84 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.83 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.9 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.85 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.88 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.89 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.87 ethambutol Not assoc w R
embB 4249673 p.Ser1054Pro missense_variant 0.74 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.88 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.81 ethambutol Not assoc w R
ethA 4328209 c.-736C>A upstream_gene_variant 0.87 ethionamide
whiB6 4338570 c.-49C>T upstream_gene_variant 0.13 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.86 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.85 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.89 streptomycin Not assoc w R
gid 4407935 p.Leu90Val missense_variant 0.86 streptomycin Uncertain significance
gid 4407944 p.Gln87Glu missense_variant 0.84 streptomycin Uncertain significance