TB-Profiler result

Run: SAMEA3231528

Summary

Run ID: SAMEA3231528

Sample name:

Date: 2024-03-26T21:06:02.460174

Number of reads: 5498640

Percentage reads mapped: 98.85

Median coverage: 159.0

Strain: lineage4.1.2.1.1

Spoligotype:

Drug-resistance: HR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.98
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) RD182 0.99
lineage4 Euro-American 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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin gid c.329_330delTG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.1900delT Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1304826 c.1900delT frameshift_variant 0.12 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
gid 4407872 c.329_330delTG frameshift_variant 0.88 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
dnaA 1434 c.1434C>A synonymous_variant 0.11 isoniazid
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 8048 c.747C>T synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8203 p.Asn301Ser missense_variant 0.12 levofloxacin
moxifloxacin
gyrA 8999 c.1698G>A synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9528 p.Gln743Glu missense_variant 0.17 levofloxacin
moxifloxacin
fgd1 490814 p.Ser11Leu missense_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575343 c.-5C>T upstream_gene_variant 0.13 ethionamide
isoniazid
mshA 575629 c.282A>G synonymous_variant 0.15 ethionamide
isoniazid
mshA 575679 p.Asn111Ser missense_variant 0.95 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575832 p.Gly162Asp missense_variant 0.3 ethionamide
isoniazid
mshA 576581 p.Pro412Ser missense_variant 0.13 ethionamide
isoniazid
mshA 576718 c.1371C>T synonymous_variant 0.13 ethionamide
isoniazid
ccsA 619693 c.-198G>A upstream_gene_variant 0.29 capreomycin
amikacin
kanamycin
ccsA 620058 c.168C>T synonymous_variant 0.14 capreomycin
amikacin
kanamycin
ccsA 620568 c.678C>T synonymous_variant 0.12 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
Rv0565c 657457 p.Pro5Arg missense_variant 0.1 ethionamide
Rv0565c 657618 c.-148T>C upstream_gene_variant 0.11 ethionamide
rpoB 760115 c.309C>T synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 760350 p.Asp182Asn missense_variant 0.13 rifampicin
rpoB 760879 p.Pro358Gln missense_variant 0.14 rifampicin
rpoB 761953 p.Ala716Val missense_variant 0.14 rifampicin
rpoC 762443 c.-927G>A upstream_gene_variant 0.12 rifampicin
rpoB 762630 p.Ala942Thr missense_variant 0.14 rifampicin Uncertain significance
rpoC 763669 c.300C>A synonymous_variant 0.12 rifampicin
rpoC 764712 p.Ala448Gly missense_variant 0.17 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 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 777793 p.Ala230Thr missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 779209 c.-729G>A upstream_gene_variant 0.18 clofazimine
bedaquiline
rpsL 781193 c.-367T>C upstream_gene_variant 0.11 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800387 c.-422C>T upstream_gene_variant 0.14 linezolid
rplC 800651 c.-158G>C upstream_gene_variant 0.13 linezolid
rplC 800658 c.-151T>A upstream_gene_variant 0.12 linezolid
Rv1129c 1253351 p.Ala395Val missense_variant 0.12 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253418 p.Ala373Thr missense_variant 0.12 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1253718 p.Ala273Thr missense_variant 0.12 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1302873 c.-58A>T upstream_gene_variant 0.12 clofazimine
pretomanid
delamanid
fbiC 1303084 p.Gly52Ser missense_variant 0.11 clofazimine
pretomanid
delamanid
fbiC 1304655 c.1725C>T synonymous_variant 0.14 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406159 c.1182G>A synonymous_variant 0.12 streptomycin
isoniazid
pyrazinamide
Rv1258c 1406539 p.Ala268Thr missense_variant 0.12 streptomycin
isoniazid
pyrazinamide
Rv1258c 1407159 p.Val61Ala missense_variant 0.14 streptomycin
isoniazid
pyrazinamide
embR 1416651 p.Thr233Ala missense_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472894 n.1049G>A non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472906 n.1061T>C non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474309 n.652G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1475181 n.1524A>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476264 n.2607A>G non_coding_transcript_exon_variant 0.1 capreomycin
linezolid
rpsA 1833426 c.-116T>C upstream_gene_variant 0.11 pyrazinamide
tsnR 1853857 c.252G>A synonymous_variant 0.14 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tsnR 1854373 c.768G>A synonymous_variant 0.12 linezolid
tlyA 1917919 c.-21C>T upstream_gene_variant 0.13 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918095 c.156G>A synonymous_variant 0.12 capreomycin
tlyA 1918182 c.243G>A synonymous_variant 0.15 capreomycin
ndh 2102394 p.Ala217Thr missense_variant 0.17 ethionamide
delamanid
isoniazid
PPE35 2168436 p.Leu726Pro missense_variant 0.11 pyrazinamide
PPE35 2169558 p.Phe352Tyr missense_variant 0.13 pyrazinamide
Rv1979c 2222204 p.Phe321Leu missense_variant 0.12 clofazimine
bedaquiline
Rv1979c 2222656 p.Lys170Thr missense_variant 0.1 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289637 c.-396G>A upstream_gene_variant 0.12 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
eis 2714543 c.790C>A synonymous_variant 0.17 amikacin
kanamycin
eis 2715209 p.Thr42Ala missense_variant 0.11 amikacin
kanamycin
folC 2746609 c.990T>C synonymous_variant 0.1 para-aminosalicylic_acid
Rv2477c 2782753 c.1290G>A synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784200 c.-158T>C upstream_gene_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784232 c.-190C>T upstream_gene_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987048 c.212delT frameshift_variant 0.17 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.32 capreomycin
Rv2680 2996523 p.Arg140Met missense_variant 0.14 capreomycin
Rv2752c 3064901 p.Leu431Met missense_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065396 p.Met266Val missense_variant 0.1 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066989 c.-798T>C upstream_gene_variant 0.15 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3074466 c.6G>A synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339029 c.-89C>T upstream_gene_variant 0.18 clofazimine
pretomanid
delamanid
Rv3236c 3612718 c.399C>T synonymous_variant 0.25 pyrazinamide
Rv3236c 3612759 p.Gly120Arg missense_variant 0.5 pyrazinamide
Rv3236c 3613106 p.Ser4Leu missense_variant 0.11 pyrazinamide
Rv3236c 3613301 c.-185G>A upstream_gene_variant 0.22 pyrazinamide
Rv3236c 3613674 c.-558G>A upstream_gene_variant 0.95 pyrazinamide
Rv3236c 3613781 c.-665C>T upstream_gene_variant 0.33 pyrazinamide
lpqB 3623693 c.1218G>T synonymous_variant 0.15 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625136 p.Arg493Gln missense_variant 0.12 bedaquiline
rifampicin
mtrB 3625188 p.Arg476Cys missense_variant 0.12 bedaquiline
rifampicin
mtrB 3625703 p.Ser304Ile missense_variant 0.12 bedaquiline
rifampicin
mtrB 3626240 p.Gly125Asp missense_variant 0.12 bedaquiline
rifampicin
mtrA 3627699 c.-350G>T upstream_gene_variant 0.2 bedaquiline
rifampicin
fbiB 3642114 p.Val194Ile missense_variant 0.22 clofazimine Uncertain significance
pretomanid
delamanid
alr 3840663 p.Pro253Arg missense_variant 0.13 cycloserine
glpK 4138575 p.Ala394Glu missense_variant 0.11 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139601 c.154delC frameshift_variant 0.15 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.96 ethambutol Not assoc w R
embC 4242642 p.Arg927His missense_variant 0.17 ethambutol Uncertain significance
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embA 4244329 p.Ala366Val missense_variant 0.13 ethambutol
embA 4244364 p.Gly378Ser missense_variant 0.12 ethambutol Uncertain significance
embA 4245114 p.Gly628Ser missense_variant 0.13 ethambutol
embA 4245213 p.Ala661Thr missense_variant 0.29 ethambutol
embA 4245907 p.Leu892Pro missense_variant 0.12 ethambutol
embA 4246195 p.Pro988His missense_variant 0.14 ethambutol
embB 4247079 p.Phe189Ser missense_variant 0.12 ethambutol
aftB 4267622 c.1215G>A synonymous_variant 0.14 ethambutol
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin