TB-Profiler result

Run: ERR4799849
Summary

Run ID: ERR4799849

Sample name:

Date: 2024-10-04T23:08:54.408640

Number of reads: 3530910

Percentage reads mapped: 99.64

Median coverage: 98.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage4 Euro-American None 0.87
lineage4.8 Euro-American (mainly T) RD219 0.87
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asn437Asp Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
pyrazinamide pncA p.Pro54Leu Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.95 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761115 p.Asn437Asp missense_variant 0.98 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761161 p.Leu452Pro missense_variant 0.96 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2289081 p.Pro54Leu missense_variant 0.83 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.95 ethambutol 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.15 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.9 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.15 ethionamide Not assoc w R - Interim
nusG 734658 c.405A>G synonymous_variant 0.92 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.13 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.13 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.18 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.13 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid 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 0.93 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.17 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.83 pyrazinamide 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.9 capreomycin
thyA 3073687 p.Ala262Val missense_variant 0.88 para-aminosalicylic_acid
thyA 3074338 p.Leu45Pro missense_variant 0.11 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.1 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.94 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.18 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.85 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.13 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
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.14 streptomycin Not assoc w R