TB-Profiler result

Run: ERR4972483
Summary

Run ID: ERR4972483

Sample name:

Date: 2024-10-04T00:05:21.981288

Number of reads: 4822828

Percentage reads mapped: 89.37

Median coverage: 164.0

Strain: lineage4.1.2.1.1

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
lineage4.1 Euro-American None 0.99
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.99
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 rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA p.Gln10Pro Assoc w R
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
gid c.329_330delTG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA p.Gln121* Assoc w R
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 7570 p.Ala90Val missense_variant 0.9 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin Assoc w R
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.85 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide Assoc w R
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol Assoc w R
ethA 4327113 p.Gln121* stop_gained 0.99 ethionamide Assoc w R
gid 4407872 c.329_330delTG frameshift_variant 0.98 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.98 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.94 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.94 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoB 762008 c.2202C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.15 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.14 rifampicin Uncertain significance
rpoB 762131 c.2325C>G synonymous_variant 0.15 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.14 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.14 rifampicin
rpoC 763067 c.-303C>G upstream_gene_variant 0.15 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.17 rifampicin
rpoC 764551 c.1182G>C synonymous_variant 0.18 rifampicin
rpoC 764554 c.1185C>T synonymous_variant 0.17 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764593 c.1224C>T synonymous_variant 0.2 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764651 p.Ser428Thr missense_variant 0.13 rifampicin
rpoC 764822 p.Asp485His missense_variant 0.86 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
rpoC 765967 c.2598C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.14 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766010 p.Ser881Thr missense_variant 0.14 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.14 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.15 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.15 rifampicin
rpoC 766054 c.2685C>G synonymous_variant 0.14 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.13 rifampicin
rpoC 766795 c.3426C>T synonymous_variant 0.14 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.15 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.15 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.14 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777793 p.Ala230Thr missense_variant 0.97 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781838 c.279G>C synonymous_variant 0.14 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.13 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474960 n.1303C>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474963 n.1306G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474964 n.1307T>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474965 n.1308G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834733 p.Ala398Ser missense_variant 0.14 pyrazinamide
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518561 c.447T>C synonymous_variant 0.14 isoniazid
kasA 2518768 c.654C>T synonymous_variant 0.14 isoniazid
kasA 2518777 c.663C>T synonymous_variant 0.14 isoniazid
Rv2477c 2782894 c.1149C>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782913 p.Ser377Thr missense_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782928 p.Thr372Lys missense_variant 0.14 kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Uncertain significance
amikacin Uncertain significance
Rv2477c 2782930 c.1113G>A synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782957 c.1086A>G synonymous_variant 0.13 kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2782966 c.1077C>A synonymous_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782972 c.1071G>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782981 c.1062G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782984 c.1059T>C synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2782990 c.1053C>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783914 c.129T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.18 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.3 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
thyX 3067515 p.Ser144Thr missense_variant 0.13 para-aminosalicylic_acid
thyX 3067577 c.369G>A synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625774 c.840G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625797 p.Val273Met missense_variant 0.15 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625806 c.808A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625807 c.807C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3878322 c.186A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.13 rifampicin
rpoA 3878364 c.144A>T synonymous_variant 0.15 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.14 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.14 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.14 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.14 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.14 rifampicin
rpoA 3878764 c.-257A>G upstream_gene_variant 0.15 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.17 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.18 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.19 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.22 rifampicin
rpoA 3878833 c.-326C>G upstream_gene_variant 0.17 rifampicin
rpoA 3878836 c.-331_-329delAAGinsTCC upstream_gene_variant 0.17 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.17 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.97 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.97 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.99 ethambutol Not assoc w R
embA 4245182 c.1950T>C synonymous_variant 0.15 ethambutol
embB 4247819 p.Val436Ile missense_variant 0.13 ethambutol Uncertain significance
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 1.0 kanamycin
capreomycin
amikacin